Variant report

Variant	rs4948093
Chromosome Location	chr7:56024287-56024288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:56022593..56025153-chr7:56159111..56161145,2	K562	blood:
2	chr7:56022690..56025113-chr7:56180352..56182821,2	K562	blood:
3	chr7:56022715..56025169-chr7:56117660..56119960,2	MCF-7	breast:
4	chr7:56023602..56026001-chr7:56031001..56033765,3	MCF-7	breast:
5	chr7:56018536..56023436-chr7:56023593..56027250,7	K562	blood:

Variant related genes	Relation type
ENSG00000146731	Chromatin interaction
ENSG00000146733	Chromatin interaction
ENSG00000164776	Chromatin interaction
ENSG00000146729	Chromatin interaction
ENSG00000239789	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10043	0.82[JPT][hapmap]
rs10236322	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10260031	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10260048	1.00[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10263766	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11238384	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11238392	0.82[JPT][hapmap]
rs11238393	0.82[JPT][hapmap]
rs11765364	1.00[ASW][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap]
rs11771756	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12538444	0.82[JPT][hapmap]
rs13230292	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13240729	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs15892	1.00[ASW][hapmap];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];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967230	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2304376	1.00[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2331096	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2331166	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2538048	1.00[ASW][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap]
rs2965455	1.00[ASW][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap]
rs35347591	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4245574	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4518614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4540366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4947528	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4947529	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4948083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4948085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4948090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948094	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55634856	0.89[ASN][1000 genomes]
rs56128104	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56207001	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56269128	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56351949	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62456630	0.97[ASN][1000 genomes]
rs62456648	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62456651	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62456653	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62456654	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6421738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6593289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6593290	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6945638	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs6946065	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6965614	1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs6970353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6972415	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6974707	1.00[ASW][hapmap];0.81[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7790255	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7794115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808729	0.82[JPT][hapmap]
rs816407	1.00[ASW][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap]
rs8406	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9649783	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
9	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
12	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4948093	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs4948093	CHCHD2	cis	multi-tissue	Pritchard
rs4948093	LOC146325	trans	lymphoblastoid	RTeQTL
rs4948093	CHCHD2	cis	parietal	SCAN
rs4948093	ZNF713	cis	cerebellum	SCAN
rs4948093	LOC645317	trans	multi-tissue	Pritchard
rs4948093	CHCHD2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56020200-56026000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:56020200-56031200	Weak transcription	Brain Substantia Nigra	brain
3	chr7:56020200-56031400	Weak transcription	Small Intestine	intestine
4	chr7:56020200-56031600	Weak transcription	Aorta	Aorta
5	chr7:56020200-56031800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:56020400-56028000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:56020400-56031000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr7:56020400-56031200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:56020400-56031200	Weak transcription	NHDF-Ad	bronchial
10	chr7:56020400-56031400	Weak transcription	Brain Angular Gyrus	brain
11	chr7:56020400-56031400	Weak transcription	Colonic Mucosa	Colon
12	chr7:56020400-56031400	Weak transcription	Colon Smooth Muscle	Colon
13	chr7:56020400-56031400	Weak transcription	Esophagus	oesophagus
14	chr7:56020400-56031400	Weak transcription	Fetal Kidney	kidney
15	chr7:56020400-56031600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:56020400-56031600	Weak transcription	Psoas Muscle	Psoas
17	chr7:56020400-56031600	Weak transcription	HUVEC	blood vessel
18	chr7:56020400-56031800	Weak transcription	HSMMtube	muscle
19	chr7:56020400-56032600	Weak transcription	Fetal Lung	lung
20	chr7:56020600-56027800	Weak transcription	Thymus	Thymus
21	chr7:56020600-56030200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:56020600-56031400	Weak transcription	Primary B cells from cord blood	blood
23	chr7:56020600-56031600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:56020600-56031800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:56020800-56025000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr7:56020800-56026600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:56020800-56031000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr7:56020800-56031000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr7:56021000-56024800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:56021000-56025600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:56021000-56031000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr7:56021000-56031000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:56021000-56031400	Weak transcription	Fetal Heart	heart
34	chr7:56021200-56024800	Strong transcription	Fetal Stomach	stomach
35	chr7:56021200-56025400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr7:56021200-56025600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:56021200-56031200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr7:56021200-56031400	Weak transcription	Fetal Brain Male	brain
39	chr7:56021800-56024400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:56021800-56024400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:56021800-56027200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr7:56021800-56031400	Weak transcription	Pancreas	Pancrea
43	chr7:56021800-56031600	Weak transcription	NHLF	lung
44	chr7:56022000-56024400	Strong transcription	Dnd41	blood
45	chr7:56022000-56031400	Weak transcription	Placenta	Placenta
46	chr7:56022000-56031600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:56022000-56031600	Weak transcription	Fetal Thymus	thymus
48	chr7:56022000-56031600	Weak transcription	Osteobl	bone
49	chr7:56022200-56027800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:56022200-56030800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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