Variant report

Variant	rs1980198
Chromosome Location	chr1:169336259-169336260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:169336053-169338642	IMR90	lung:	n/a	n/a
2	MXI1	chr1:169336098-169338754	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169075479..169078672-chr1:169335264..169338570,4	MCF-7	breast:
2	chr1:169073561..169077593-chr1:169336088..169341683,7	K562	blood:
3	chr1:169335832..169338194-chr1:169763167..169765301,2	K562	blood:

Variant related genes	Relation type
BLZF1	TF binding region
ENSG00000143153	Chromatin interaction
ENSG00000000460	Chromatin interaction
ENSG00000171806	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10429893	0.85[CEU][hapmap];0.80[YRI][hapmap]
rs10458395	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10458396	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10458397	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753786	0.82[MEX][hapmap]
rs10800439	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800441	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800446	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919132	0.82[MEX][hapmap]
rs10919154	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919164	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919167	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1112839	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11800843	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs12022776	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023892	0.81[ASN][1000 genomes]
rs12024897	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12026287	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12026996	0.86[CHB][hapmap]
rs12027242	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12029853	0.86[CHB][hapmap]
rs12030320	0.86[CHB][hapmap]
rs12033253	0.86[CHB][hapmap]
rs12034986	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12037211	0.86[CHB][hapmap]
rs12038609	0.86[CHB][hapmap]
rs12043489	0.86[CHB][hapmap]
rs12563090	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12564884	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1400836	0.85[CEU][hapmap]
rs1400838	0.81[ASN][1000 genomes]
rs1415928	0.86[CHB][hapmap]
rs1517748	1.00[ASN][1000 genomes]
rs1589113	0.86[CHB][hapmap]
rs16862172	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs2003652	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003654	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2014061	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2235195	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs2268048	0.86[CHB][hapmap]
rs2275299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753303	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766089	0.86[CHB][hapmap]
rs3766095	0.85[CEU][hapmap]
rs3766096	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905328	0.85[CEU][hapmap]
rs4656183	0.82[CEU][hapmap]
rs4656670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656672	0.85[CEU][hapmap]
rs6427185	0.85[CEU][hapmap]
rs6427186	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427188	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6427189	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6660945	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6677410	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696428	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696810	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72702156	0.81[ASN][1000 genomes]
rs7516248	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7528375	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528449	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537890	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7539415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554703	0.95[AFR][1000 genomes]
rs961404	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS 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	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1980198	NME7	cis	Thyroid	GTEx
rs1980198	CELF6	trans	cerebellum	SCAN
rs1980198	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs1980198	C1orf114	cis	cerebellum	SCAN
rs1980198	F5	cis	cerebellum	SCAN
rs1980198	BLZF1	cis	Whole Blood	GTEx
rs1980198	SELP	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
3	chr1:169309400-169336400	Weak transcription	Ovary	ovary
4	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
6	chr1:169330000-169336400	Weak transcription	Psoas Muscle	Psoas
7	chr1:169330800-169336400	Weak transcription	Right Ventricle	heart
8	chr1:169332200-169336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:169332800-169336400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:169333200-169336400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:169333200-169336400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:169334200-169336400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:169334200-169336600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:169334600-169336400	Weak transcription	Placenta	Placenta
15	chr1:169334800-169336400	Weak transcription	Fetal Intestine Small	intestine
16	chr1:169334800-169336400	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:169335600-169336400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:169335600-169336400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:169335600-169338200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:169335800-169336400	Enhancers	Primary T cells from cord blood	blood
21	chr1:169335800-169336400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:169335800-169336400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr1:169335800-169336400	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr1:169335800-169336400	Enhancers	Fetal Heart	heart
25	chr1:169335800-169336400	Enhancers	Fetal Intestine Large	intestine
26	chr1:169335800-169336400	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:169335800-169336400	Enhancers	NH-A	brain
28	chr1:169335800-169336600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:169335800-169336600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:169335800-169336600	Enhancers	Small Intestine	intestine
31	chr1:169335800-169336800	Flanking Active TSS	Fetal Lung	lung
32	chr1:169335800-169336800	Weak transcription	Gastric	stomach
33	chr1:169335800-169336800	Flanking Active TSS	Dnd41	blood
34	chr1:169335800-169337000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:169335800-169337800	Active TSS	Fetal Brain Female	brain
36	chr1:169335800-169338200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:169335800-169338400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:169335800-169338400	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr1:169335800-169338400	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr1:169335800-169338600	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr1:169335800-169338600	Active TSS	K562	blood
42	chr1:169335800-169339000	Active TSS	NHLF	lung
43	chr1:169336000-169336400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:169336000-169336400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:169336000-169336400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:169336000-169336400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:169336000-169336400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr1:169336000-169336400	Enhancers	Brain Cingulate Gyrus	brain
49	chr1:169336000-169336400	Enhancers	GM12878-XiMat	blood
50	chr1:169336000-169336400	Flanking Active TSS	HepG2	liver

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