Variant report

Variant	rs1154597
Chromosome Location	chr3:119736833-119736834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119736409..119738702-chr3:119741738..119744184,2	MCF-7	breast:
2	chr3:119736524..119739259-chr3:119742014..119746399,5	K562	blood:
3	chr3:119730742..119733006-chr3:119735849..119738068,2	MCF-7	breast:
4	chr3:119736313..119739253-chr3:119813749..119816280,3	MCF-7	breast:
5	chr3:119735441..119737549-chr3:119811971..119814912,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10049256	0.87[CEU][hapmap]
rs10934512	0.87[CEU][hapmap]
rs1154596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11921053	1.00[ASN][1000 genomes]
rs12152218	0.87[CEU][hapmap]
rs13312998	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314595	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1488764	0.87[CEU][hapmap]
rs1626696	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16830683	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];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16830689	1.00[CHB][hapmap]
rs1719887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1719888	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719889	1.00[CHB][hapmap]
rs1719895	1.00[ASW][hapmap];0.87[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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1732165	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1732169	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs182839	0.90[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];0.81[YRI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs184576	0.85[EUR][1000 genomes]
rs1907681	0.87[CEU][hapmap]
rs2035671	0.87[CEU][hapmap]
rs2035674	0.87[CEU][hapmap]
rs2037547	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2130000	0.87[CEU][hapmap]
rs2319541	0.87[CEU][hapmap]
rs2319543	0.87[CEU][hapmap]
rs2461827	0.91[ASN][1000 genomes]
rs2874022	0.85[CEU][hapmap]
rs2874023	0.87[CEU][hapmap]
rs3108749	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334534	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];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334535	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs334536	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs334538	0.84[CHD][hapmap]
rs334539	0.87[CEU][hapmap]
rs334545	0.81[ASW][hapmap];0.87[CEU][hapmap]
rs334549	0.87[CEU][hapmap]
rs334551	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs334552	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334554	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334559	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs334560	0.94[ASN][1000 genomes]
rs334561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334565	0.81[YRI][hapmap]
rs334566	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3853592	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072520	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4438691	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4488869	0.87[CEU][hapmap]
rs4605584	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4676822	0.87[CEU][hapmap]
rs4688043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56126162	0.84[ASN][1000 genomes]
rs58043853	0.81[ASN][1000 genomes]
rs60272712	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438555	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6438558	0.87[CEU][hapmap]
rs6438559	0.87[CEU][hapmap]
rs6438564	0.85[CEU][hapmap]
rs6438567	0.87[CEU][hapmap]
rs66650215	0.97[ASN][1000 genomes]
rs6762640	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764549	0.86[CEU][hapmap]
rs6769435	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs6769988	0.87[CEU][hapmap]
rs6770314	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs6771023	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6774693	1.00[ASN][1000 genomes]
rs6776122	0.87[CEU][hapmap]
rs6779828	1.00[CHB][hapmap]
rs6781470	0.87[CEU][hapmap]
rs6784239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790751	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6794478	0.85[CEU][hapmap]
rs6795874	0.84[ASN][1000 genomes]
rs6797689	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];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6805931	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6807868	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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613197	0.84[ASN][1000 genomes]
rs7617372	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7620750	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs7624540	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7628426	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7635604	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636600	1.00[ASN][1000 genomes]
rs7644268	0.87[CEU][hapmap]
rs7650554	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];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7652172	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7653263	0.85[CEU][hapmap]
rs7653396	0.85[CEU][hapmap]
rs902790	0.87[CEU][hapmap]
rs902791	0.87[CEU][hapmap]
rs902794	0.87[CEU][hapmap]
rs902795	0.87[CEU][hapmap]
rs923380	0.87[CEU][hapmap]
rs923726	0.87[CEU][hapmap]
rs923727	0.87[CEU][hapmap]
rs923728	0.87[CEU][hapmap]
rs9289138	0.84[ASN][1000 genomes]
rs9289143	0.87[CEU][hapmap]
rs968824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9784393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs979682	0.87[CEU][hapmap]
rs9813834	0.87[CEU][hapmap]
rs9829763	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9842302	0.87[CEU][hapmap]
rs9851174	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9853082	0.87[CEU][hapmap]
rs9858566	0.87[CEU][hapmap]
rs9859778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9879992	1.00[CHB][hapmap];0.84[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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119712600-119745000	Weak transcription	Hela-S3	cervix
2	chr3:119713200-119744400	Weak transcription	Fetal Kidney	kidney
3	chr3:119720200-119741000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:119720400-119737200	Weak transcription	NHDF-Ad	bronchial
5	chr3:119720800-119738600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:119723600-119740600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:119724000-119738200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:119724000-119741400	Weak transcription	Thymus	Thymus
9	chr3:119730000-119743000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:119730000-119743000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:119730600-119739200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:119730600-119740800	Weak transcription	Left Ventricle	heart
13	chr3:119730600-119741600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:119731000-119741400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:119731400-119752400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:119731600-119737200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:119731800-119737000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:119731800-119739800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:119732000-119739400	Weak transcription	Ovary	ovary
20	chr3:119732200-119747200	Weak transcription	Gastric	stomach
21	chr3:119732200-119747600	Weak transcription	Right Ventricle	heart
22	chr3:119732600-119737000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:119732600-119738200	Weak transcription	Fetal Heart	heart
24	chr3:119732600-119739200	Weak transcription	Brain Anterior Caudate	brain
25	chr3:119732600-119739200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:119732600-119740800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:119732600-119741600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:119732600-119748400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:119732600-119748600	Weak transcription	HSMM	muscle
30	chr3:119732600-119757800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:119732800-119746200	Weak transcription	Fetal Lung	lung
32	chr3:119732800-119749200	Weak transcription	Fetal Stomach	stomach
33	chr3:119733000-119747400	Weak transcription	Right Atrium	heart
34	chr3:119733200-119744200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:119733400-119739000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:119733400-119741600	Weak transcription	Osteobl	bone
37	chr3:119733600-119739200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:119733800-119739400	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:119734000-119739400	Weak transcription	Brain Substantia Nigra	brain
40	chr3:119734000-119740400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:119734200-119741000	Weak transcription	Primary T cells from cord blood	blood
42	chr3:119734600-119737400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:119734800-119737800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:119734800-119738200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:119734800-119750000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:119735000-119739400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:119735000-119751600	Weak transcription	Primary B cells from cord blood	blood
48	chr3:119735200-119741000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:119735200-119742800	Weak transcription	Fetal Brain Female	brain
50	chr3:119735400-119737000	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links