Variant report

Variant	rs13312998
Chromosome Location	chr3:119666266-119666267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119659377..119662242-chr3:119664934..119667462,2	MCF-7	breast:
2	chr3:119665679..119667853-chr3:119671736..119673872,2	K562	blood:
3	chr3:119623117..119624885-chr3:119665357..119667174,2	MCF-7	breast:
4	chr3:119662709..119665581-chr3:119665685..119667851,2	MCF-7	breast:
5	chr3:119664595..119667160-chr3:119811953..119814918,2	K562	blood:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1154596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1154597	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]
rs11921053	1.00[ASN][1000 genomes]
rs13314595	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1626696	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16830683	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];0.81[AFR][1000 genomes];0.92[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]
rs1719888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1719889	1.00[CHB][hapmap]
rs1719895	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1732165	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1732169	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs182839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2035674	0.87[CEU][hapmap]
rs2037547	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2461816	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs2461827	0.91[ASN][1000 genomes]
rs2472680	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs3108749	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334534	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];0.81[AFR][1000 genomes];0.92[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	0.87[CEU][hapmap]
rs334549	0.87[CEU][hapmap]
rs334551	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs334552	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334554	0.92[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];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334566	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3853592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072520	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4438691	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4605584	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4688043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56126162	0.84[ASN][1000 genomes]
rs58043853	0.81[ASN][1000 genomes]
rs60272712	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438550	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6438554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.85[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]
rs66650215	0.97[ASN][1000 genomes]
rs6762640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769435	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
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]
rs6779828	1.00[CHB][hapmap]
rs6781470	0.87[CEU][hapmap]
rs6784239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790751	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6795874	0.84[ASN][1000 genomes]
rs6797689	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];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6805931	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6807868	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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[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	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7635604	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636600	1.00[ASN][1000 genomes]
rs7644268	0.87[CEU][hapmap]
rs7650554	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];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7652172	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs902795	0.87[CEU][hapmap]
rs923380	0.87[CEU][hapmap]
rs9289138	0.84[ASN][1000 genomes]
rs968824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9784393	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9829763	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9851174	1.00[CHB][hapmap];1.00[CHD][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:4 , 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	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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
4	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:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:119611200-119667000	Weak transcription	Pancreas	Pancrea
3	chr3:119611400-119682200	Weak transcription	HSMMtube	muscle
4	chr3:119625000-119668200	Weak transcription	Hela-S3	cervix
5	chr3:119629600-119672200	Weak transcription	Fetal Stomach	stomach
6	chr3:119630800-119697400	Weak transcription	Thymus	Thymus
7	chr3:119631000-119717000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:119635000-119667000	Weak transcription	Placenta	Placenta
9	chr3:119636400-119667200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:119640600-119672400	Weak transcription	Osteobl	bone
11	chr3:119641000-119681600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:119641000-119681600	Weak transcription	Fetal Intestine Small	intestine
13	chr3:119641000-119694400	Weak transcription	Fetal Lung	lung
14	chr3:119641200-119666400	Weak transcription	HepG2	liver
15	chr3:119641200-119681200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:119645400-119669600	Weak transcription	Psoas Muscle	Psoas
17	chr3:119650200-119669800	Weak transcription	Liver	Liver
18	chr3:119650400-119669600	Weak transcription	Left Ventricle	heart
19	chr3:119653600-119669600	Weak transcription	Ovary	ovary
20	chr3:119656400-119669400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:119656400-119680600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:119656400-119681200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:119656400-119700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:119656600-119669800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:119656600-119718400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:119658000-119669800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:119658200-119669000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:119658200-119669400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:119658200-119669600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:119658400-119669400	Weak transcription	Brain Angular Gyrus	brain
31	chr3:119658400-119688400	Weak transcription	NHEK	skin
32	chr3:119658400-119688600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:119658800-119667000	Weak transcription	Stomach Mucosa	stomach
34	chr3:119661000-119667000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:119662000-119684800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:119662400-119700400	Weak transcription	Fetal Intestine Large	intestine
37	chr3:119663200-119669600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:119663400-119666400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:119663600-119669400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:119663600-119681200	Weak transcription	Primary T cells from cord blood	blood
41	chr3:119663800-119666400	Strong transcription	Dnd41	blood
42	chr3:119664000-119669600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:119664000-119695000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:119664200-119668400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:119664200-119674400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:119664400-119666400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:119664400-119666400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr3:119664400-119666400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:119664600-119673600	Weak transcription	Small Intestine	intestine
50	chr3:119664600-119700200	Weak transcription	Rectal Mucosa Donor 31	rectum

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