Variant report

Variant	rs17177358
Chromosome Location	chr7:139456812-139456813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs1015121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224408	0.83[CEU][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs10230692	0.91[EUR][1000 genomes]
rs10254826	0.96[EUR][1000 genomes]
rs10268753	0.91[EUR][1000 genomes]
rs10278124	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs1106768	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12374780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177103	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177953	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes]
rs17262390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17262662	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17262676	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074826	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs4074827	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs55826011	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56079671	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56840127	0.93[EUR][1000 genomes]
rs61054086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967634	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73158611	0.96[EUR][1000 genomes]
rs73158613	0.96[EUR][1000 genomes]
rs73158614	0.96[EUR][1000 genomes]
rs73158616	0.95[EUR][1000 genomes]
rs73735624	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs740818	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787807	0.96[EUR][1000 genomes]
rs7793114	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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
rs17177358	LOC730441	cis	parietal	SCAN
rs17177358	RAB19	cis	parietal	SCAN
rs17177358	TBXAS1	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139432200-139461800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:139432400-139458600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:139432800-139469800	Weak transcription	Hela-S3	cervix
4	chr7:139438400-139462800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr7:139438400-139467000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr7:139438600-139462600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:139438800-139466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr7:139439000-139462800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr7:139440600-139457600	Enhancers	Brain Substantia Nigra	brain
10	chr7:139440600-139474600	Weak transcription	Fetal Brain Male	brain
11	chr7:139441000-139458400	Enhancers	Brain Hippocampus Middle	brain
12	chr7:139442400-139462000	Weak transcription	HUVEC	blood vessel
13	chr7:139444000-139466000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr7:139444600-139462600	Weak transcription	NHEK	skin
15	chr7:139445800-139460600	Weak transcription	HMEC	breast
16	chr7:139445800-139466000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr7:139446600-139459000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr7:139446600-139475800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:139446600-139476400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:139446800-139476400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:139448400-139465400	Weak transcription	Primary B cells from cord blood	blood
22	chr7:139448600-139461200	Weak transcription	Aorta	Aorta
23	chr7:139449200-139466600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr7:139451400-139466000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:139451800-139458000	Enhancers	Liver	Liver
26	chr7:139451800-139458200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr7:139452200-139460600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:139453000-139460600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:139453200-139466800	Weak transcription	Thymus	Thymus
30	chr7:139453400-139461200	Weak transcription	Fetal Lung	lung
31	chr7:139453600-139462400	Weak transcription	Fetal Kidney	kidney
32	chr7:139453600-139467600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr7:139453800-139458400	Genic enhancers	Muscle Satellite Cultured Cells	--
34	chr7:139453800-139462400	Weak transcription	NHDF-Ad	bronchial
35	chr7:139453800-139462600	Weak transcription	Spleen	Spleen
36	chr7:139453800-139462600	Weak transcription	NH-A	brain
37	chr7:139454000-139457600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:139454000-139457800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr7:139454000-139461000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:139454000-139462000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:139454000-139462600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr7:139454000-139462800	Weak transcription	Placenta	Placenta
43	chr7:139454000-139467600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr7:139454200-139462600	Weak transcription	HSMMtube	muscle
45	chr7:139454200-139463000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr7:139454200-139471000	Weak transcription	Brain Germinal Matrix	brain
47	chr7:139454200-139474000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr7:139454400-139457400	Weak transcription	Small Intestine	intestine
49	chr7:139454400-139458000	Weak transcription	Fetal Intestine Large	intestine
50	chr7:139454400-139461000	Weak transcription	Adipose Nuclei	Adipose

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