Variant report

Variant	rs821397
Chromosome Location	chr1:86103097-86103098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10747323	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10747324	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs10873711	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10873718	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[EUR][1000 genomes]
rs10873719	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[EUR][1000 genomes]
rs1094353	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1094360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12037294	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405017	0.87[CHD][hapmap]
rs12410234	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12756841	0.84[EUR][1000 genomes]
rs12757797	0.83[YRI][hapmap]
rs12758966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360239	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1481200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1617458	0.85[ASN][1000 genomes]
rs17128293	0.92[ASN][1000 genomes]
rs1764287	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1764295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775987	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1775989	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1775991	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs1775992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775993	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2014733	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2014750	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[EUR][1000 genomes]
rs2026772	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2026773	0.81[ASW][hapmap]
rs2026774	0.93[ASW][hapmap];1.00[CHD][hapmap];0.83[YRI][hapmap]
rs2389973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2389974	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2389975	0.91[EUR][1000 genomes]
rs2773131	0.83[AFR][1000 genomes]
rs2785082	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2970548	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313723	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs313724	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs313725	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[ASN][1000 genomes]
rs369999	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs381453	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[EUR][1000 genomes]
rs383558	0.87[EUR][1000 genomes]
rs399547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs401657	0.91[YRI][hapmap];0.87[EUR][1000 genomes]
rs420515	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs425357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs429040	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs430956	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes]
rs432254	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[EUR][1000 genomes]
rs4379699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs438401	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes]
rs444875	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs450953	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes]
rs4949917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4949918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs550329	0.81[YRI][hapmap]
rs6673975	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes]
rs6682235	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[EUR][1000 genomes]
rs6686719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6694808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7521240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7528385	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7529942	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[EUR][1000 genomes]
rs7533395	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7535884	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[EUR][1000 genomes]
rs7547023	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[EUR][1000 genomes]
rs7554621	0.84[EUR][1000 genomes]
rs821377	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs821378	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs821380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs821382	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs821383	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821385	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs821387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821390	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs821392	0.83[EUR][1000 genomes]
rs821400	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];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821402	0.93[ASW][hapmap]
rs821403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs821404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs849158	0.82[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324152	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.80[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9324153	0.93[ASW][hapmap]
rs9651138	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9661608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9701898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9793556	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];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1000290	chr1:86078495-86105379	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs821397	ZNHIT6	cis	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86083800-86103200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:86091200-86103200	Weak transcription	Brain Angular Gyrus	brain
3	chr1:86091800-86107600	Weak transcription	Colonic Mucosa	Colon
4	chr1:86094000-86118600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:86094800-86103200	Weak transcription	Small Intestine	intestine
6	chr1:86095000-86103200	Weak transcription	Fetal Heart	heart
7	chr1:86095200-86104200	Weak transcription	Psoas Muscle	Psoas
8	chr1:86095200-86104400	Weak transcription	Right Ventricle	heart
9	chr1:86095400-86107600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:86095400-86119000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:86095600-86103800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:86095600-86104000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:86095600-86104000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:86095600-86117000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:86095800-86103200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:86096000-86104000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:86096200-86103400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:86096200-86103800	Weak transcription	HepG2	liver
20	chr1:86096200-86115600	Weak transcription	NH-A	brain
21	chr1:86096400-86104800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:86096600-86103200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:86099800-86103800	Strong transcription	Primary T cells from cord blood	blood
24	chr1:86101000-86107600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:86101200-86106600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr1:86101400-86103600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:86101800-86103200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:86101800-86103200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:86101800-86103400	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:86101800-86103600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr1:86101800-86103600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
32	chr1:86101800-86103600	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr1:86101800-86103600	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:86101800-86103600	ZNF genes & repeats	Thymus	Thymus
35	chr1:86102000-86103200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr1:86102000-86103600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:86102000-86104200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:86102000-86105200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
39	chr1:86102200-86103600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:86102200-86104800	Weak transcription	Fetal Brain Male	brain
41	chr1:86102400-86103400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:86102400-86103600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
43	chr1:86102400-86103600	ZNF genes & repeats	HSMM	muscle
44	chr1:86102400-86104000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:86102400-86105200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:86102400-86105200	ZNF genes & repeats	Primary B cells from cord blood	blood
47	chr1:86102400-86105400	ZNF genes & repeats	Dnd41	blood
48	chr1:86102600-86103200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:86102600-86103400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:86102600-86103600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links