Variant report

Variant	rs2525731
Chromosome Location	chr7:120619292-120619293
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120617320..120619610-chr7:120694736..120697163,2	K562	blood:
2	chr7:120614613..120620636-chr7:120722021..120725742,5	K562	blood:

Variant related genes	Relation type
ENSG00000212628	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10229719	0.85[EUR][1000 genomes]
rs10258025	0.81[EUR][1000 genomes]
rs11363	0.96[EUR][1000 genomes]
rs12672149	0.83[EUR][1000 genomes]
rs13881	0.95[EUR][1000 genomes]
rs193727	0.84[EUR][1000 genomes]
rs2074576	0.94[EUR][1000 genomes]
rs2215786	0.86[EUR][1000 genomes]
rs2215789	0.84[EUR][1000 genomes]
rs2525711	0.94[EUR][1000 genomes]
rs2525714	0.94[EUR][1000 genomes]
rs2525715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525716	0.94[EUR][1000 genomes]
rs2525717	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs2525718	0.94[EUR][1000 genomes]
rs2525720	0.94[EUR][1000 genomes]
rs2525722	0.94[EUR][1000 genomes]
rs2525723	0.94[EUR][1000 genomes]
rs2525724	0.94[EUR][1000 genomes]
rs2525725	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525726	0.94[EUR][1000 genomes]
rs2525728	0.96[EUR][1000 genomes]
rs2525732	0.97[EUR][1000 genomes]
rs2525733	0.97[EUR][1000 genomes]
rs2525734	0.97[EUR][1000 genomes]
rs2525735	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2525738	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2525739	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2525740	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2721350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721351	0.94[EUR][1000 genomes]
rs2721359	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2721361	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2721366	1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs2721368	0.94[EUR][1000 genomes]
rs2721370	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896299	0.83[EUR][1000 genomes]
rs3944026	0.90[EUR][1000 genomes]
rs41691	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41692	0.84[EUR][1000 genomes]
rs41693	0.84[EUR][1000 genomes]
rs41694	0.84[EUR][1000 genomes]
rs41695	0.84[EUR][1000 genomes]
rs41697	0.84[EUR][1000 genomes]
rs41703	0.81[EUR][1000 genomes]
rs41704	0.81[EUR][1000 genomes]
rs4727915	0.85[EUR][1000 genomes]
rs4730985	0.85[EUR][1000 genomes]
rs6966297	0.88[EUR][1000 genomes]
rs6973457	0.90[EUR][1000 genomes]
rs73429864	0.86[ASN][1000 genomes]
rs7789501	0.85[EUR][1000 genomes]
rs7808535	0.85[EUR][1000 genomes]
rs886440	1.00[CHB][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
rs2525731	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120591600-120627800	Weak transcription	Pancreas	Pancrea
2	chr7:120592400-120621600	Weak transcription	Aorta	Aorta
3	chr7:120592400-120628000	Weak transcription	Stomach Mucosa	stomach
4	chr7:120604400-120621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:120608200-120621800	Weak transcription	NHEK	skin
6	chr7:120608600-120627600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:120609400-120622400	Weak transcription	Gastric	stomach
8	chr7:120609400-120627800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:120609400-120627800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:120609400-120628600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:120611600-120619400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:120611600-120619400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:120611600-120620000	Weak transcription	Fetal Heart	heart
14	chr7:120611600-120621800	Weak transcription	HMEC	breast
15	chr7:120611600-120622000	Weak transcription	Fetal Intestine Small	intestine
16	chr7:120611600-120622200	Weak transcription	HSMMtube	muscle
17	chr7:120611600-120624000	Weak transcription	Fetal Brain Male	brain
18	chr7:120611600-120626200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:120611600-120627400	Weak transcription	Brain Angular Gyrus	brain
20	chr7:120611600-120627600	Weak transcription	Fetal Muscle Leg	muscle
21	chr7:120611600-120627600	Weak transcription	Fetal Stomach	stomach
22	chr7:120611600-120627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:120611600-120627800	Weak transcription	Esophagus	oesophagus
24	chr7:120611600-120627800	Weak transcription	Thymus	Thymus
25	chr7:120611800-120619800	Weak transcription	A549	lung
26	chr7:120611800-120620200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:120611800-120620400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr7:120611800-120621800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:120615000-120627600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr7:120615200-120619600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:120615200-120621800	Weak transcription	GM12878-XiMat	blood
32	chr7:120615400-120619600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:120615400-120619800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr7:120615400-120620400	Weak transcription	Fetal Brain Female	brain
35	chr7:120615400-120621800	Weak transcription	K562	blood
36	chr7:120615400-120627800	Weak transcription	Colonic Mucosa	Colon
37	chr7:120615400-120628000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:120615600-120620000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:120615600-120621600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:120615600-120621800	Weak transcription	Brain Substantia Nigra	brain
41	chr7:120615600-120622000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr7:120615600-120622000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:120615600-120624400	Weak transcription	Hela-S3	cervix
44	chr7:120615600-120627400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr7:120615600-120627600	Weak transcription	Brain Anterior Caudate	brain
46	chr7:120615600-120627800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:120615600-120627800	Weak transcription	Colon Smooth Muscle	Colon
48	chr7:120615600-120627800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr7:120615600-120628000	Weak transcription	Small Intestine	intestine
50	chr7:120615800-120627800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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