Variant report

Variant	rs17136728
Chromosome Location	chr7:102989726-102989727
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102983625..102990524-chr7:102994295..102998538,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161057	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10245155	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10257369	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs10266523	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10268808	0.94[CEU][hapmap]
rs10271758	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10486853	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs11978339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17136078	0.87[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs17136079	0.87[CEU][hapmap]
rs17136083	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs17606134	0.82[JPT][hapmap]
rs17680523	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs17837510	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs1861731	0.87[CEU][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap]
rs1968201	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs2193420	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs2878	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3087615	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs4266582	0.87[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs4593456	0.87[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs4727563	0.87[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs4727566	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs4727568	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4729887	0.87[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs4729891	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs4729896	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs4729899	0.86[CEU][hapmap]
rs4729902	0.87[CEU][hapmap]
rs5025411	0.84[GIH][hapmap];0.82[JPT][hapmap]
rs62481648	0.82[EUR][1000 genomes]
rs62481655	0.88[EUR][1000 genomes]
rs62482371	0.88[EUR][1000 genomes]
rs62482396	0.98[EUR][1000 genomes]
rs62482404	1.00[ASN][1000 genomes]
rs62482405	0.96[ASN][1000 genomes]
rs62482406	1.00[ASN][1000 genomes]
rs6971734	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6972190	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73175852	0.96[ASN][1000 genomes]
rs7455141	0.87[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs7777392	0.87[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs7804020	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS 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	46 gene(s)	inside rSNPs	diseases
2	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17136728	ZNF655	cis	parietal	SCAN
rs17136728	RP11-401L13.5	cis	Thyroid	GTEx
rs17136728	ZNF789	cis	cerebellum	SCAN
rs17136728	PSMC2	cis	parietal	SCAN
rs17136728	DNAJC2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102987400-102989800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr7:102987400-102990000	Active TSS	NHLF	lung
3	chr7:102987400-102990400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:102987600-102989800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr7:102987600-102989800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:102987600-102989800	Active TSS	Right Atrium	heart
7	chr7:102987600-102990000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:102987600-102990000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr7:102987600-102990000	Active TSS	Colonic Mucosa	Colon
10	chr7:102987600-102990000	Active TSS	Psoas Muscle	Psoas
11	chr7:102987800-102989800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr7:102987800-102989800	Active TSS	Fetal Stomach	stomach
13	chr7:102987800-102989800	Active TSS	A549	lung
14	chr7:102987800-102990000	Active TSS	GM12878-XiMat	blood
15	chr7:102988000-102989800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:102988000-102990000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:102988000-102990600	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr7:102988400-102989800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:102988600-102989800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr7:102988600-102990000	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr7:102988600-102990800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr7:102988600-103002400	Weak transcription	Spleen	Spleen
23	chr7:102988800-102989800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:102988800-102989800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr7:102988800-102989800	Enhancers	Fetal Heart	heart
26	chr7:102988800-102990000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr7:102988800-102990000	Flanking Active TSS	Dnd41	blood
28	chr7:102988800-102990200	Flanking Active TSS	Liver	Liver
29	chr7:102988800-102990400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:102989000-102989800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr7:102989000-102989800	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr7:102989000-102989800	Flanking Active TSS	Hela-S3	cervix
33	chr7:102989000-102990000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:102989000-102990000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr7:102989000-102990000	Flanking Active TSS	HUVEC	blood vessel
36	chr7:102989000-102990200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:102989000-102990200	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr7:102989000-102990800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr7:102989000-103006200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr7:102989200-102989800	Weak transcription	Pancreas	Pancrea
41	chr7:102989200-102989800	Flanking Active TSS	NH-A	brain
42	chr7:102989200-102989800	Flanking Active TSS	Osteobl	bone
43	chr7:102989200-102990000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr7:102989200-102990000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:102989200-102990000	Enhancers	Small Intestine	intestine
46	chr7:102989200-102990000	Flanking Active TSS	NHEK	skin
47	chr7:102989200-102990200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr7:102989200-102990200	Enhancers	Left Ventricle	heart
49	chr7:102989200-102990200	Enhancers	Lung	lung
50	chr7:102989200-102990800	Enhancers	Primary neutrophils fromperipheralblood	blood

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