Variant report

Variant	rs17262662
Chromosome Location	chr7:139468767-139468768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:139458332..139460713-chr7:139467552..139469581,2	MCF-7	breast:
2	chr7:139328993..139331448-chr7:139467533..139470371,3	K562	blood:
3	chr7:139467872..139470323-chr7:139609014..139611111,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1015121	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224408	0.90[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs10230692	0.90[EUR][1000 genomes]
rs10254826	0.92[EUR][1000 genomes]
rs10268753	0.90[EUR][1000 genomes]
rs10278124	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs1106768	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155449	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374779	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12374780	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177103	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177358	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177953	0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17262390	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17262676	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074826	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs4074827	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs55826011	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56079671	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56840127	0.88[EUR][1000 genomes]
rs61054086	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967634	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73158611	0.92[EUR][1000 genomes]
rs73158613	0.92[EUR][1000 genomes]
rs73158614	0.92[EUR][1000 genomes]
rs73158616	0.91[EUR][1000 genomes]
rs73735624	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs740818	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787807	0.92[EUR][1000 genomes]
rs7793114	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798740	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020234	chr7:139377822-139661964	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032711	chr7:139411404-139684043	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv464732	chr7:139424022-139654256	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv608472	chr7:139424022-139654256	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1018712	chr7:139429703-139658014	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17262662	RAB19	cis	parietal	SCAN
rs17262662	TBXAS1	cis	parietal	SCAN
rs17262662	LOC730441	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139432800-139469800	Weak transcription	Hela-S3	cervix
2	chr7:139440600-139474600	Weak transcription	Fetal Brain Male	brain
3	chr7:139446600-139475800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr7:139446600-139476400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:139446800-139476400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:139454200-139471000	Weak transcription	Brain Germinal Matrix	brain
7	chr7:139454200-139474000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr7:139455000-139475000	Weak transcription	Fetal Intestine Small	intestine
9	chr7:139455200-139473400	Weak transcription	Fetal Brain Female	brain
10	chr7:139458200-139471400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:139459600-139474400	Weak transcription	Fetal Intestine Large	intestine
12	chr7:139461600-139471200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:139463000-139469800	Weak transcription	A549	lung
14	chr7:139463200-139469200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:139463200-139472000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr7:139463600-139475000	Weak transcription	Ovary	ovary
17	chr7:139463800-139469200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:139463800-139470400	Weak transcription	NH-A	brain
19	chr7:139463800-139471000	Weak transcription	HSMMtube	muscle
20	chr7:139463800-139471200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:139464000-139469400	Weak transcription	HMEC	breast
22	chr7:139464000-139470800	Weak transcription	NHDF-Ad	bronchial
23	chr7:139464200-139470200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr7:139465200-139470000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:139465200-139470800	Genic enhancers	Muscle Satellite Cultured Cells	--
26	chr7:139465400-139469200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr7:139465400-139469600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr7:139465400-139470000	Enhancers	Right Ventricle	heart
29	chr7:139465600-139469600	Enhancers	Brain Hippocampus Middle	brain
30	chr7:139465600-139470000	Enhancers	Fetal Heart	heart
31	chr7:139465600-139475000	Enhancers	Brain Substantia Nigra	brain
32	chr7:139465800-139470000	Strong transcription	Fetal Stomach	stomach
33	chr7:139466200-139469200	Enhancers	Pancreas	Pancrea
34	chr7:139466200-139469200	Enhancers	Right Atrium	heart
35	chr7:139466200-139470000	Enhancers	Primary T cells fromperipheralblood	blood
36	chr7:139466400-139469000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:139466400-139469200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:139466400-139469200	Enhancers	Gastric	stomach
39	chr7:139466400-139469400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:139466400-139469400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:139466600-139469000	Enhancers	Stomach Mucosa	stomach
42	chr7:139466600-139469400	Enhancers	Duodenum Mucosa	Duodenum
43	chr7:139466600-139469600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr7:139466600-139469800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:139466600-139472200	Enhancers	Brain Anterior Caudate	brain
46	chr7:139466800-139468800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr7:139466800-139469000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr7:139466800-139469000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr7:139466800-139469000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:139466800-139469200	Enhancers	Thymus	Thymus

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