Variant report

Variant	rs1932978
Chromosome Location	chr1:146727763-146727764
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:146727066..146728772-chr1:146732769..146735404,2	K562	blood:
2	chr1:146727066..146728885-chr1:146732769..146735404,3	K562	blood:
3	chr1:146639513..146641119-chr1:146727207..146729004,2	MCF-7	breast:
4	chr1:146726179..146728330-chr1:146735798..146738089,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10159076	0.86[JPT][hapmap]
rs1036852	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs1047140	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs10751402	0.96[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs10793652	0.85[CEU][hapmap];0.84[AMR][1000 genomes]
rs10793653	0.81[AMR][1000 genomes]
rs10900314	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs10900315	0.85[CEU][hapmap]
rs10900319	0.86[JPT][hapmap]
rs10900322	0.81[EUR][1000 genomes]
rs10900326	0.85[CEU][hapmap]
rs10900331	0.86[JPT][hapmap]
rs1123333	0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.81[ASN][1000 genomes]
rs11239950	0.80[AMR][1000 genomes]
rs11239951	0.81[AMR][1000 genomes]
rs11239953	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239955	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239956	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023638	0.86[JPT][hapmap]
rs12023644	0.86[JPT][hapmap]
rs12024575	0.86[JPT][hapmap]
rs12031956	0.86[JPT][hapmap]
rs12038539	0.86[JPT][hapmap]
rs12039400	0.86[JPT][hapmap]
rs12040321	0.86[JPT][hapmap]
rs12049109	0.86[JPT][hapmap]
rs12092016	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12093458	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12736102	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13375602	0.86[JPT][hapmap]
rs1348316	0.81[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs1442758	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1442760	0.96[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1470261	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs1470262	0.89[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.81[ASN][1000 genomes]
rs17359526	0.85[CEU][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs1837983	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1837984	0.96[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1890041	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1899485	0.89[CEU][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap]
rs2078325	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs2297751	0.86[JPT][hapmap]
rs2354442	0.96[CEU][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap]
rs3766521	0.86[JPT][hapmap]
rs4274116	0.80[ASN][1000 genomes]
rs4950378	0.96[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4950390	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4950391	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6593738	0.96[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6593750	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6593752	0.88[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6657665	0.86[JPT][hapmap]
rs6670503	0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[MEX][hapmap]
rs6674562	0.86[JPT][hapmap]
rs6680845	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6681716	0.86[JPT][hapmap]
rs6687016	0.85[CEU][hapmap]
rs6690158	0.86[JPT][hapmap]
rs6693631	0.85[CEU][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs6694020	0.86[JPT][hapmap]
rs6704497	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71510594	0.81[AMR][1000 genomes]
rs7512450	0.86[JPT][hapmap]
rs7519377	0.86[JPT][hapmap]
rs7519804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7548820	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9988435	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
4	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
6	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
7	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
15	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
17	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
20	nsv437047	chr1:146643555-146841602	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
21	nsv1005809	chr1:146647822-146886419	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv535134	chr1:146647822-146886419	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
23	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
24	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
25	nsv547676	chr1:146686228-146996047	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1932978	CHD1L	Cis_1M	lymphoblastoid	RTeQTL
rs1932978	CHD1L	cis	cerebellum	SCAN
rs1932978	CHD1L	cis	Whole Blood	GTEx
rs1932978	RNF115	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146715600-146736200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:146715600-146749400	Weak transcription	Colonic Mucosa	Colon
3	chr1:146715800-146731400	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:146715800-146756800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:146716000-146731600	Weak transcription	Fetal Kidney	kidney
6	chr1:146716000-146731800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:146716000-146732400	Weak transcription	Aorta	Aorta
8	chr1:146716000-146732400	Weak transcription	Fetal Brain Male	brain
9	chr1:146716000-146735600	Weak transcription	Ovary	ovary
10	chr1:146716000-146739600	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:146716000-146743800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:146716200-146727800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:146716200-146732200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:146716400-146732200	Weak transcription	NHLF	lung
15	chr1:146716600-146731400	Weak transcription	Fetal Brain Female	brain
16	chr1:146716800-146731000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:146716800-146748600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:146717200-146751000	Weak transcription	Gastric	stomach
19	chr1:146717600-146730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:146717600-146736600	Weak transcription	Psoas Muscle	Psoas
21	chr1:146717800-146732800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:146719200-146730000	Weak transcription	HMEC	breast
23	chr1:146719200-146730800	Weak transcription	HSMM	muscle
24	chr1:146719200-146731400	Weak transcription	Right Ventricle	heart
25	chr1:146719400-146731000	Weak transcription	Brain Substantia Nigra	brain
26	chr1:146719400-146731800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:146719400-146736400	Weak transcription	Brain Angular Gyrus	brain
28	chr1:146719400-146757600	Weak transcription	Stomach Mucosa	stomach
29	chr1:146719600-146727800	Weak transcription	Fetal Lung	lung
30	chr1:146719600-146731600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:146719600-146736200	Weak transcription	Spleen	Spleen
32	chr1:146719600-146747600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:146719600-146747800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:146719600-146748000	Weak transcription	Small Intestine	intestine
35	chr1:146719800-146729600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:146719800-146729800	Weak transcription	Brain Anterior Caudate	brain
37	chr1:146719800-146731400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:146719800-146731800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:146719800-146732000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:146719800-146732600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:146719800-146732800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:146722200-146740200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:146722400-146731400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:146722400-146731800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:146722400-146740200	Weak transcription	Pancreas	Pancrea
46	chr1:146722600-146732400	Weak transcription	Lung	lung
47	chr1:146722600-146749400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:146722800-146769800	Strong transcription	Dnd41	blood
49	chr1:146723600-146730600	Strong transcription	Primary B cells from cord blood	blood
50	chr1:146723800-146727800	Strong transcription	HepG2	liver

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