Variant report

Variant	rs2525717
Chromosome Location	chr7:120602831-120602832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120596918..120600663-chr7:120601555..120604578,6	MCF-7	breast:
2	chr7:120589597..120593785-chr7:120599349..120604596,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10258025	0.81[EUR][1000 genomes]
rs11363	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013087	0.83[CEU][hapmap]
rs2074576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074577	0.94[CEU][hapmap]
rs2215786	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2215789	1.00[CEU][hapmap]
rs2244863	0.94[CEU][hapmap]
rs2244865	0.94[CEU][hapmap]
rs2525711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525712	0.94[CEU][hapmap]
rs2525713	0.94[CEU][hapmap]
rs2525714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2525715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs2525716	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525719	1.00[CEU][hapmap]
rs2525720	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525723	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes]
rs2525726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525731	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs2525732	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2525735	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2525738	1.00[CEU][hapmap]
rs2525739	1.00[CEU][hapmap]
rs2525740	1.00[CEU][hapmap]
rs2721350	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2721351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721363	0.84[CEU][hapmap]
rs2721366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes]
rs2721372	1.00[CEU][hapmap]
rs2896299	0.83[CEU][hapmap]
rs3944026	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs41688	0.94[CEU][hapmap]
rs41691	1.00[CEU][hapmap]
rs41692	1.00[CEU][hapmap]
rs41694	1.00[CEU][hapmap]
rs41697	1.00[CEU][hapmap]
rs41703	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs41704	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4727915	0.83[CEU][hapmap]
rs4727917	0.80[CEU][hapmap]
rs4730985	0.82[CEU][hapmap]
rs6966297	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6973457	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7808535	0.82[CEU][hapmap]

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	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2525717	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120591600-120606600	Weak transcription	Lung	lung
2	chr7:120591600-120608000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:120591600-120608000	Weak transcription	Esophagus	oesophagus
4	chr7:120591600-120608000	Weak transcription	Gastric	stomach
5	chr7:120591600-120608000	Weak transcription	Spleen	Spleen
6	chr7:120591600-120611200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:120591600-120612800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:120591600-120613200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr7:120591600-120613200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:120591600-120627800	Weak transcription	Pancreas	Pancrea
11	chr7:120591800-120606400	Weak transcription	Ovary	ovary
12	chr7:120591800-120618600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr7:120592200-120611000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:120592400-120606400	Weak transcription	Fetal Brain Male	brain
15	chr7:120592400-120606400	Weak transcription	NHEK	skin
16	chr7:120592400-120607800	Weak transcription	HSMMtube	muscle
17	chr7:120592400-120608000	Weak transcription	Psoas Muscle	Psoas
18	chr7:120592400-120614800	Weak transcription	Small Intestine	intestine
19	chr7:120592400-120617000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr7:120592400-120618600	Weak transcription	Right Ventricle	heart
21	chr7:120592400-120621600	Weak transcription	Aorta	Aorta
22	chr7:120592400-120628000	Weak transcription	Stomach Mucosa	stomach
23	chr7:120593000-120604600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:120593000-120606400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr7:120594400-120608000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:120594800-120609000	Weak transcription	NH-A	brain
27	chr7:120595000-120610800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:120595200-120608000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr7:120595600-120608000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:120595600-120608000	Weak transcription	Fetal Intestine Small	intestine
31	chr7:120596000-120608000	Weak transcription	HepG2	liver
32	chr7:120596200-120604800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr7:120596400-120604600	Weak transcription	Fetal Brain Female	brain
34	chr7:120596400-120608000	Weak transcription	Colonic Mucosa	Colon
35	chr7:120596600-120604800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:120596600-120604800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr7:120596600-120606000	Weak transcription	HMEC	breast
38	chr7:120596600-120606400	Weak transcription	Brain Substantia Nigra	brain
39	chr7:120596600-120606400	Weak transcription	NHLF	lung
40	chr7:120596600-120607800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr7:120596600-120607800	Weak transcription	NHDF-Ad	bronchial
42	chr7:120596600-120608000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:120596800-120603600	Weak transcription	Dnd41	blood
44	chr7:120596800-120604800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr7:120596800-120605000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr7:120596800-120606400	Weak transcription	Hela-S3	cervix
47	chr7:120596800-120606600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:120596800-120607800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr7:120596800-120607800	Weak transcription	A549	lung
50	chr7:120597200-120604400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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