Variant report

Variant	rs9817377
Chromosome Location	chr3:196284063-196284064
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196282210..196288763-chr3:196290964..196297416,8	K562	blood:
2	chr3:196283744..196286438-chr3:196295350..196297318,2	MCF-7	breast:
3	chr3:196283678..196289168-chr3:196293009..196297108,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185798	Chromatin interaction
ENSG00000174013	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11185544	0.84[CEU][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.84[ASN][1000 genomes]
rs11185545	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1124996	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11706197	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11707537	0.80[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs11711952	0.84[ASN][1000 genomes]
rs11714694	0.84[ASN][1000 genomes]
rs11920455	0.81[ASN][1000 genomes]
rs12494859	0.88[AMR][1000 genomes]
rs12495687	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs1355533	0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs2054748	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054749	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054750	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2086891	0.84[CEU][hapmap];0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs2137193	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2341334	0.81[ASN][1000 genomes]
rs2341399	0.84[CEU][hapmap];0.87[CHD][hapmap];0.91[TSI][hapmap]
rs28479172	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2880030	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34292861	0.94[EUR][1000 genomes]
rs3964310	0.84[ASN][1000 genomes]
rs4488870	0.84[ASN][1000 genomes]
rs4916433	0.93[EUR][1000 genomes]
rs56144237	0.81[ASN][1000 genomes]
rs57365032	0.86[AMR][1000 genomes]
rs60668021	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62410583	0.86[AMR][1000 genomes]
rs6583318	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6765975	0.84[ASN][1000 genomes]
rs6775806	0.84[ASN][1000 genomes]
rs6778889	0.87[CHD][hapmap]
rs6780633	0.84[ASN][1000 genomes]
rs6780856	0.84[ASN][1000 genomes]
rs6799694	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6799697	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73219653	0.84[ASN][1000 genomes]
rs73219654	0.84[ASN][1000 genomes]
rs73219660	0.84[ASN][1000 genomes]
rs7615547	0.84[ASN][1000 genomes]
rs7619117	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7621684	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7623111	0.84[ASN][1000 genomes]
rs7626039	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7638562	1.00[JPT][hapmap]
rs9311	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9647412	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9647413	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811428	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9813420	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814342	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9818507	0.84[ASN][1000 genomes]
rs9828786	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9831225	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839347	0.84[ASN][1000 genomes]
rs9839388	0.88[CEU][hapmap]
rs9840938	0.84[ASN][1000 genomes]
rs9843607	0.93[EUR][1000 genomes]
rs9848622	0.88[CEU][hapmap]
rs9849530	0.84[ASN][1000 genomes]
rs9853777	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9854347	0.86[AMR][1000 genomes]
rs9858251	0.86[AMR][1000 genomes]
rs9868492	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9870613	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
11	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196272600-196287400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:196272600-196288000	Weak transcription	K562	blood
3	chr3:196274200-196286800	Weak transcription	Liver	Liver
4	chr3:196276800-196293800	Weak transcription	HepG2	liver
5	chr3:196277000-196285800	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:196277400-196285400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr3:196277600-196284800	Weak transcription	Thymus	Thymus
8	chr3:196277600-196287800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:196277600-196290200	Weak transcription	NH-A	brain
10	chr3:196277600-196294200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:196277800-196285800	Weak transcription	Aorta	Aorta
12	chr3:196277800-196287600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:196277800-196287600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:196277800-196287800	Weak transcription	Fetal Brain Female	brain
15	chr3:196277800-196293600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:196278000-196286000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:196278000-196286400	Weak transcription	Fetal Stomach	stomach
18	chr3:196278000-196287600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:196278000-196287600	Weak transcription	HSMMtube	muscle
20	chr3:196278000-196294400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:196278200-196287400	Weak transcription	NHDF-Ad	bronchial
22	chr3:196278200-196288200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:196278400-196287800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:196278600-196285000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:196278600-196286600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:196278600-196287800	Weak transcription	Osteobl	bone
27	chr3:196278800-196285800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:196278800-196287800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:196278800-196294600	Weak transcription	Gastric	stomach
30	chr3:196279000-196286600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:196279000-196287400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:196279000-196287400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:196279000-196287800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:196279000-196289400	Weak transcription	Hela-S3	cervix
35	chr3:196279000-196294000	Weak transcription	Brain Anterior Caudate	brain
36	chr3:196279000-196294200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:196279200-196285000	Weak transcription	Placenta	Placenta
38	chr3:196279200-196285600	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:196279200-196286000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:196279200-196286200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:196279200-196286400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:196279200-196286800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:196279200-196294000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:196279200-196294400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:196279400-196286200	Weak transcription	Ovary	ovary
46	chr3:196279400-196287800	Weak transcription	Pancreas	Pancrea
47	chr3:196279400-196294200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:196279600-196285000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:196279600-196286000	Weak transcription	Fetal Kidney	kidney
50	chr3:196279600-196286200	Weak transcription	Stomach Smooth Muscle	stomach

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