Variant report

Variant	rs9833162
Chromosome Location	chr3:136035737-136035738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135915139..135916754-chr3:136035024..136037890,2	K562	blood:
2	chr3:136033614..136036060-chr3:136051639..136053164,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10513002	1.00[CHB][hapmap]
rs10935178	1.00[CHB][hapmap]
rs12330258	0.84[AFR][1000 genomes]
rs1279425	0.81[YRI][hapmap]
rs16843879	1.00[CHB][hapmap]
rs16843978	1.00[CHB][hapmap]
rs16843991	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap]
rs17199978	1.00[CHB][hapmap]
rs17266364	1.00[CHB][hapmap]
rs28396702	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28812220	0.93[EUR][1000 genomes]
rs34165586	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523567	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35058853	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35644083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs3755636	0.81[YRI][hapmap]
rs3872588	1.00[CHB][hapmap]
rs5026242	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55797013	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56251259	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap]
rs67214626	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6766450	0.83[EUR][1000 genomes]
rs6773604	1.00[CHB][hapmap]
rs6776841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781817	1.00[CHB][hapmap]
rs6783337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785225	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6800570	1.00[CHB][hapmap]
rs6804194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620314	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs7622833	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7650075	1.00[CHB][hapmap]
rs9809184	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811261	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9811490	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812513	1.00[CEU][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9819496	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826146	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[EUR][1000 genomes]
rs9831321	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9843348	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9843801	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9850383	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9853387	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9854328	0.81[EUR][1000 genomes]
rs9860801	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9868120	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs9872326	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv4025	chr3:136017458-136065622	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135970600-136039400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:135981200-136052000	Weak transcription	NH-A	brain
3	chr3:135998000-136040200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:135999800-136038200	Weak transcription	Fetal Brain Male	brain
5	chr3:135999800-136061200	Weak transcription	Hela-S3	cervix
6	chr3:136000200-136038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:136014200-136040000	Weak transcription	Small Intestine	intestine
8	chr3:136015000-136038800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:136016400-136038400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:136016800-136045600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:136017000-136040000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:136018200-136051400	Weak transcription	A549	lung
13	chr3:136019000-136038600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:136020200-136036400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:136020200-136039000	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:136020200-136040200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:136020200-136045200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:136020400-136038400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:136020400-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:136020400-136045200	Weak transcription	Colonic Mucosa	Colon
21	chr3:136020600-136035800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:136020600-136035800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:136020600-136035800	Weak transcription	Aorta	Aorta
24	chr3:136020600-136035800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:136020600-136036000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:136020600-136036200	Weak transcription	Lung	lung
27	chr3:136020600-136036400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:136020600-136038000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:136020600-136038200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:136020600-136045000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:136020600-136045200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:136020800-136035800	Weak transcription	Fetal Lung	lung
33	chr3:136020800-136035800	Weak transcription	Ovary	ovary
34	chr3:136020800-136036200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:136020800-136037400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:136020800-136040200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:136020800-136040200	Weak transcription	Esophagus	oesophagus
38	chr3:136020800-136042200	Weak transcription	Placenta	Placenta
39	chr3:136020800-136043000	Weak transcription	HSMM	muscle
40	chr3:136020800-136045000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:136021000-136035800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:136021000-136035800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:136021000-136036000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:136021000-136036000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:136021000-136036200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:136021000-136036200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:136021000-136036400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:136021000-136036600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr3:136021000-136038600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:136021000-136038600	Weak transcription	Right Ventricle	heart

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