Variant report

Variant	rs1042657
Chromosome Location	chr17:38173792-38173793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38173721-38174772	GM12892	blood:	n/a	n/a
2	POLR2A	chr17:38173011-38174885	K562	blood:	n/a	n/a
3	POLR2A	chr17:38173369-38174229	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr17:38173672-38174318	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr17:38173574-38174006	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr17:38170916-38176213	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr17:38170766-38176716	U87	brain:	n/a	n/a
8	POLR2A	chr17:38170628-38176722	U87	brain:	n/a	n/a
9	POLR2A	chr17:38171303-38175657	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr17:38173296-38175247	K562	blood:	n/a	n/a
11	POLR2A	chr17:38171205-38176070	U87	brain:	n/a	n/a
12	POLR2A	chr17:38173792-38174160	GM12878	blood:	n/a	n/a
13	POLR2A	chr17:38173594-38174081	K562	blood:	n/a	n/a
14	POLR2A	chr17:38173172-38174674	Hela-S3	cervix:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38173133..38174723-chr17:38181069..38183425,2	K562	blood:
2	chr17:38171795..38174739-chr17:38253717..38256695,2	K562	blood:
3	chr17:38172520..38175725-chr17:38187607..38191443,4	MCF-7	breast:
4	chr17:38169328..38171805-chr17:38172299..38175519,5	K562	blood:
5	chr17:38172859..38176802-chr17:38178682..38181500,4	K562	blood:
6	chr17:38173047..38175621-chr17:38177692..38179979,3	MCF-7	breast:
7	chr17:38171100..38173173-chr17:38173231..38176436,3	K562	blood:
8	chr17:38171930..38174052-chr17:38295398..38298227,2	MCF-7	breast:
9	chr17:38143597..38146360-chr17:38172431..38175405,3	K562	blood:
10	chr17:38172636..38175341-chr17:38255721..38258482,3	MCF-7	breast:
11	chr17:38172905..38174715-chr17:38255635..38257887,2	MCF-7	breast:
12	chr17:38169328..38171032-chr17:38172943..38175519,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265799	TF binding region
ENSG00000108342	Chromatin interaction
ENSG00000108349	Chromatin interaction
ENSG00000265799	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000126368	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10852937	0.86[CHB][hapmap]
rs11652139	1.00[YRI][hapmap]
rs12938879	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2071369	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]
rs2071370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227324	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227338	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302775	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2302778	0.94[ASN][1000 genomes]
rs3826330	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3859190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3916061	0.88[EUR][1000 genomes]
rs3934886	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4795411	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4795417	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4795421	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6503532	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs921651	1.00[CHB][hapmap]
rs9748108	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9899955	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9900199	0.87[EUR][1000 genomes]
rs9903987	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9913632	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[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:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38155000-38174000	Weak transcription	Fetal Brain Female	brain
2	chr17:38166800-38173800	Weak transcription	Primary T cells from cord blood	blood
3	chr17:38166800-38174600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr17:38166800-38177400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:38167000-38174800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr17:38169600-38175000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr17:38169800-38175600	Enhancers	Fetal Lung	lung
10	chr17:38169800-38176000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:38170000-38174000	Weak transcription	Brain Germinal Matrix	brain
12	chr17:38170000-38174200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:38170000-38174600	Enhancers	Fetal Muscle Leg	muscle
14	chr17:38170000-38175200	Weak transcription	Brain Angular Gyrus	brain
15	chr17:38170000-38175600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr17:38170000-38176000	Enhancers	Ovary	ovary
17	chr17:38170000-38178800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr17:38170200-38173800	Weak transcription	Brain Anterior Caudate	brain
19	chr17:38170200-38174400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr17:38170200-38174600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr17:38170200-38175400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr17:38170200-38175600	Weak transcription	Brain Substantia Nigra	brain
23	chr17:38170200-38175800	Weak transcription	Primary B cells from cord blood	blood
24	chr17:38170400-38173800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:38170400-38173800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr17:38170400-38173800	Weak transcription	Brain Hippocampus Middle	brain
27	chr17:38170400-38174200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr17:38170400-38174200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr17:38170400-38174200	Enhancers	Stomach Smooth Muscle	stomach
30	chr17:38170400-38174600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr17:38170400-38175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:38170400-38175200	Weak transcription	Fetal Brain Male	brain
33	chr17:38170400-38175200	Weak transcription	Dnd41	blood
34	chr17:38170400-38177600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr17:38170400-38181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr17:38171000-38173800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr17:38171000-38174000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr17:38171000-38174000	Weak transcription	Left Ventricle	heart
39	chr17:38171000-38174200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:38171000-38174200	Weak transcription	NHDF-Ad	bronchial
41	chr17:38171000-38174400	Weak transcription	Esophagus	oesophagus
42	chr17:38171000-38174600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr17:38171000-38175200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr17:38171200-38175600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:38171400-38174200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr17:38171400-38174200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr17:38171400-38174400	Weak transcription	NH-A	brain
48	chr17:38171400-38174600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
50	chr17:38171600-38173800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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