Variant report

Variant	rs2071369
Chromosome Location	chr17:38172305-38172306
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	chr17:38171847-38172393	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr17:38170916-38176213	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr17:38170766-38176716	U87	brain:	n/a	n/a
4	REST	chr17:38171520-38173265	U87	brain:	n/a	chr17:38172955-38172964
5	POLR2A	chr17:38170628-38176722	U87	brain:	n/a	n/a
6	POLR2A	chr17:38171303-38175657	MCF10A-Er-Src	breast:	n/a	n/a
7	ZNF263	chr17:38172141-38172453	HEK293-T-REx	kidney:	n/a	chr17:38172242-38172251 chr17:38172213-38172234 chr17:38172243-38172264
8	POLR2A	chr17:38171205-38176070	U87	brain:	n/a	n/a
9	POLR2A	chr17:38170517-38172349	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr17:38170768-38172358	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr17:38171806-38172403	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38171795..38174739-chr17:38253717..38256695,2	K562	blood:
2	chr17:38169401..38172627-chr17:38277979..38280708,3	K562	blood:
3	chr17:38169328..38171805-chr17:38172299..38175519,5	K562	blood:
4	chr17:38170232..38173097-chr17:38181812..38184113,4	MCF-7	breast:
5	chr17:38170609..38173071-chr17:38181273..38184131,2	MCF-7	breast:
6	chr17:38171930..38174052-chr17:38295398..38298227,2	MCF-7	breast:
7	chr17:38082095..38085117-chr17:38171214..38173786,3	K562	blood:
8	chr17:38082350..38085117-chr17:38171214..38173786,2	K562	blood:

Variant related genes	Relation type
ENSG00000265799	TF binding region
ENSG00000008838	Chromatin interaction
ENSG00000264968	Chromatin interaction
ENSG00000238793	Chromatin interaction
ENSG00000108349	Chromatin interaction
ENSG00000172057	Chromatin interaction
ENSG00000108342	Chromatin interaction
ENSG00000265799	Chromatin interaction
ENSG00000188895	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1042657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852937	0.86[CHB][hapmap]
rs12938879	0.88[EUR][1000 genomes]
rs2071370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302775	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2302778	0.94[ASN][1000 genomes]
rs3826330	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs3859190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.86[EUR][1000 genomes]
rs3916061	0.83[EUR][1000 genomes]
rs3934886	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4795411	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs4795417	0.88[EUR][1000 genomes]
rs4795421	0.91[EUR][1000 genomes]
rs6503532	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503534	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7503939	0.94[ASN][1000 genomes]
rs8068253	0.91[EUR][1000 genomes]
rs921651	1.00[CHB][hapmap]
rs9748108	0.95[EUR][1000 genomes]
rs9899955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9900199	0.82[EUR][1000 genomes]
rs9903987	0.88[EUR][1000 genomes]
rs9913632	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking 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	28 gene(s)	inside rSNPs	diseases
2	nsv908220	chr17:38153473-38175426	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38154800-38173600	Weak transcription	Thymus	Thymus
2	chr17:38155000-38173600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:38155000-38174000	Weak transcription	Fetal Brain Female	brain
4	chr17:38166800-38173400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr17:38166800-38173800	Weak transcription	Primary T cells from cord blood	blood
6	chr17:38166800-38174600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr17:38166800-38177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr17:38167000-38174800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr17:38169200-38172400	Enhancers	NHEK	skin
12	chr17:38169600-38172400	Enhancers	Stomach Mucosa	stomach
13	chr17:38169600-38172600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr17:38169600-38173200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:38169600-38175000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr17:38169800-38172400	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr17:38169800-38173000	Enhancers	Fetal Stomach	stomach
18	chr17:38169800-38175600	Enhancers	Fetal Lung	lung
19	chr17:38169800-38176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr17:38170000-38173200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:38170000-38173600	Enhancers	Fetal Muscle Trunk	muscle
22	chr17:38170000-38174000	Weak transcription	Brain Germinal Matrix	brain
23	chr17:38170000-38174200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:38170000-38174600	Enhancers	Fetal Muscle Leg	muscle
25	chr17:38170000-38175200	Weak transcription	Brain Angular Gyrus	brain
26	chr17:38170000-38175600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr17:38170000-38176000	Enhancers	Ovary	ovary
28	chr17:38170000-38178800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr17:38170200-38172400	Enhancers	Fetal Intestine Large	intestine
30	chr17:38170200-38172400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr17:38170200-38172800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:38170200-38173000	Enhancers	Pancreas	Pancrea
33	chr17:38170200-38173800	Weak transcription	Brain Anterior Caudate	brain
34	chr17:38170200-38174400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr17:38170200-38174600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr17:38170200-38175400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr17:38170200-38175600	Weak transcription	Brain Substantia Nigra	brain
38	chr17:38170200-38175800	Weak transcription	Primary B cells from cord blood	blood
39	chr17:38170400-38172600	Enhancers	Colonic Mucosa	Colon
40	chr17:38170400-38173800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:38170400-38173800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr17:38170400-38173800	Weak transcription	Brain Hippocampus Middle	brain
43	chr17:38170400-38174200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr17:38170400-38174200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr17:38170400-38174200	Enhancers	Stomach Smooth Muscle	stomach
46	chr17:38170400-38174600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr17:38170400-38175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr17:38170400-38175200	Weak transcription	Fetal Brain Male	brain
49	chr17:38170400-38175200	Weak transcription	Dnd41	blood
50	chr17:38170400-38177600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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