Variant report

Variant	rs334535
Chromosome Location	chr3:119792304-119792305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119790905..119792563-chr3:119799334..119801591,2	MCF-7	breast:
2	chr3:119792020..119796349-chr3:119811485..119815699,5	K562	blood:
3	chr3:119790138..119793520-chr3:119812637..119815168,3	K562	blood:
4	chr3:119789871..119792489-chr3:119795247..119796872,2	K562	blood:
5	chr3:119791224..119794073-chr3:119813064..119815641,4	MCF-7	breast:
6	chr3:119790797..119794267-chr3:119811448..119815142,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10433404	0.92[YRI][hapmap]
rs10934502	0.92[YRI][hapmap]
rs10934503	0.92[YRI][hapmap]
rs10934505	0.92[YRI][hapmap]
rs10934506	0.92[YRI][hapmap]
rs10934507	0.91[YRI][hapmap]
rs1154596	1.00[CHB][hapmap]
rs1154597	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11915717	0.92[YRI][hapmap]
rs11921053	0.91[EUR][1000 genomes]
rs12629015	0.92[YRI][hapmap]
rs12634476	0.92[YRI][hapmap]
rs12634889	0.85[YRI][hapmap]
rs12638973	0.92[YRI][hapmap]
rs13312998	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs13314595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1574154	0.92[YRI][hapmap]
rs1579031	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16830683	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs16830689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719889	0.85[AFR][1000 genomes]
rs1719895	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs182839	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs184576	0.82[ASN][1000 genomes]
rs1870931	0.92[YRI][hapmap]
rs28516957	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108749	1.00[CHB][hapmap]
rs334533	0.82[CEU][hapmap]
rs334534	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs334536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334538	0.84[CHD][hapmap]
rs334552	0.84[ASN][1000 genomes]
rs334554	0.84[ASN][1000 genomes]
rs334559	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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334560	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334561	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs334566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4072520	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[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4340737	0.92[YRI][hapmap]
rs4688046	0.92[YRI][hapmap]
rs4688047	0.92[YRI][hapmap]
rs4688054	0.92[YRI][hapmap]
rs56126162	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58043853	0.91[EUR][1000 genomes]
rs6438554	1.00[CHB][hapmap]
rs6438555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66650215	0.82[EUR][1000 genomes]
rs6769435	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6771023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6774693	0.98[EUR][1000 genomes]
rs6775397	0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs6779828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784239	1.00[CHB][hapmap]
rs6785050	1.00[CHB][hapmap]
rs6795874	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6797689	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs6802301	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805931	0.84[ASN][1000 genomes]
rs6807868	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7613197	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617372	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];0.95[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7620750	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7624540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs7628426	0.84[ASN][1000 genomes]
rs7636600	0.93[EUR][1000 genomes]
rs7644234	0.82[CEU][hapmap]
rs7649661	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7650554	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs7652172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289138	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs968824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9851174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	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
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119760200-119805400	Weak transcription	HMEC	breast
2	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119768800-119792800	Weak transcription	Fetal Stomach	stomach
4	chr3:119769200-119804400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:119771400-119809400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:119771800-119805400	Weak transcription	NHEK	skin
7	chr3:119773200-119807600	Weak transcription	Right Ventricle	heart
8	chr3:119775800-119796000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:119775800-119797600	Weak transcription	Fetal Thymus	thymus
10	chr3:119778800-119796000	Weak transcription	NHDF-Ad	bronchial
11	chr3:119778800-119796400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:119779400-119804200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:119779400-119807400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:119779600-119793000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:119779600-119800200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:119779600-119807800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:119779800-119793000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:119780600-119807800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:119784400-119796400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:119784400-119797200	Weak transcription	Thymus	Thymus
21	chr3:119785400-119796800	Weak transcription	Dnd41	blood
22	chr3:119786600-119794800	Weak transcription	Hela-S3	cervix
23	chr3:119786600-119796000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:119786600-119797600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:119788000-119793000	Weak transcription	GM12878-XiMat	blood
26	chr3:119788400-119795800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:119788400-119796200	Weak transcription	Adipose Nuclei	Adipose
28	chr3:119788400-119805400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:119788400-119808600	Weak transcription	Primary B cells from cord blood	blood
30	chr3:119789400-119797000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:119789400-119809200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:119789800-119797200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:119789800-119807800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:119790000-119793800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:119790000-119797800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:119790000-119807600	Weak transcription	Liver	Liver
37	chr3:119790200-119796000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:119790200-119805000	Weak transcription	HepG2	liver
39	chr3:119790400-119794800	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:119790400-119796000	Weak transcription	Fetal Lung	lung
41	chr3:119790400-119800000	Weak transcription	Spleen	Spleen
42	chr3:119790400-119800600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:119790400-119805200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:119790600-119796000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:119790600-119797200	Weak transcription	Primary T cells from cord blood	blood
46	chr3:119790600-119797600	Weak transcription	Right Atrium	heart
47	chr3:119790600-119797800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:119790600-119807400	Weak transcription	Brain Substantia Nigra	brain
49	chr3:119790600-119807800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:119790600-119809200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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