Variant report

Variant	rs9295909
Chromosome Location	chr6:30674655-30674656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30674546-30674739	K562	blood:	n/a	n/a
2	POLR2A	chr6:30674610-30674672	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:30674157-30675744	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30657343..30659554-chr6:30673396..30677307,4	MCF-7	breast:
2	chr6:30582039..30584873-chr6:30673580..30675821,2	K562	blood:
3	chr6:30652587..30660257-chr6:30673612..30681352,12	MCF-7	breast:

Variant related genes	Relation type
MDC1	TF binding region
ENSG00000146112	Chromatin interaction
ENSG00000137404	Chromatin interaction
ENSG00000222894	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1079687	0.90[ASN][1000 genomes]
rs1109146	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16867852	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16897781	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16897791	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2075015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239886	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2269702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269707	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2285321	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2394392	0.90[ASN][1000 genomes]
rs28986465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094090	0.90[ASN][1000 genomes]
rs3132595	0.90[ASN][1000 genomes]
rs3132608	0.90[ASN][1000 genomes]
rs59378621	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61486053	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61733213	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6900113	0.81[AFR][1000 genomes]
rs6924270	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6929626	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6929698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931293	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937357	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7762626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773711	0.87[AFR][1000 genomes]
rs9295901	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295902	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295904	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9295905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295907	0.82[AMR][1000 genomes]
rs9295908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461620	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461622	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9461623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461624	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468803	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468805	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468807	0.93[ASN][1000 genomes]
rs9468811	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468812	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9468813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468814	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9501338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501481	0.92[ASN][1000 genomes]
rs9501482	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9501483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9501484	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30659200-30684200	Weak transcription	Right Atrium	heart
2	chr6:30659400-30675800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:30659400-30684400	Weak transcription	Stomach Mucosa	stomach
4	chr6:30659600-30680600	Weak transcription	Fetal Heart	heart
5	chr6:30659600-30684200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:30659600-30684200	Weak transcription	Fetal Brain Male	brain
7	chr6:30659600-30684800	Weak transcription	Small Intestine	intestine
8	chr6:30659800-30674800	Weak transcription	GM12878-XiMat	blood
9	chr6:30663200-30677000	Weak transcription	NHDF-Ad	bronchial
10	chr6:30663200-30677400	Weak transcription	Fetal Kidney	kidney
11	chr6:30663200-30678600	Weak transcription	HMEC	breast
12	chr6:30663400-30677400	Weak transcription	NH-A	brain
13	chr6:30663800-30674800	Weak transcription	Hela-S3	cervix
14	chr6:30666200-30683000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr6:30666200-30683000	Strong transcription	Fetal Muscle Leg	muscle
16	chr6:30666200-30683000	Strong transcription	Fetal Stomach	stomach
17	chr6:30666200-30683800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:30666400-30682600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:30666400-30683200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:30666400-30683200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:30666600-30675400	Strong transcription	Fetal Thymus	thymus
22	chr6:30666600-30680600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:30666800-30683400	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:30667200-30683000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:30667200-30683200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:30667400-30676400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr6:30667400-30680000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:30667400-30683000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:30667400-30683000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:30667600-30683000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:30667600-30683200	Strong transcription	Dnd41	blood
32	chr6:30668000-30677000	Strong transcription	Thymus	Thymus
33	chr6:30668400-30684400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr6:30668600-30679000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr6:30668600-30682000	Strong transcription	Fetal Intestine Small	intestine
36	chr6:30669200-30674800	Strong transcription	Liver	Liver
37	chr6:30669200-30679600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:30669200-30681800	Strong transcription	Brain Germinal Matrix	brain
39	chr6:30669200-30682800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:30669200-30683200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:30669200-30683200	Strong transcription	Placenta	Placenta
42	chr6:30669600-30679600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:30669600-30679800	Strong transcription	Primary B cells from peripheral blood	blood
44	chr6:30669800-30682600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:30669800-30683000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:30670000-30675000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:30670000-30676200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:30670000-30677400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:30670000-30682400	Strong transcription	Brain Anterior Caudate	brain
50	chr6:30670000-30683200	Strong transcription	Primary T cells from cord blood	blood

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