Variant report

Variant	rs10232372
Chromosome Location	chr7:30627518-30627519
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	chr7:30626513..30628428-chr7:30630630..30632224,2	MCF-7	breast:
2	chr7:30626599..30629714-chr7:30633718..30636578,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106105	Chromatin interaction
ENSG00000196295	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10227133	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10233132	0.81[ASN][1000 genomes]
rs10237725	0.85[EUR][1000 genomes]
rs10239660	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10243040	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249885	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10265589	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10480088	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074373	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951271	0.83[ASN][1000 genomes]
rs1141114	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761080	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532057	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12533961	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13228758	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1468402	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1558064	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16875282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16875285	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009662	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214837	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240401	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267710	0.84[ASN][1000 genomes]
rs2270025	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391870	0.81[EUR][1000 genomes]
rs3779250	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3807632	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722999	0.86[ASN][1000 genomes]
rs6462211	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6947982	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6970688	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970807	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9648369	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1024458	chr7:30601877-30649659	Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10232372	AC005154.6	cis	Thyroid	GTEx
rs10232372	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs10232372	AC005154.6	cis	Nerve Tibial	GTEx
rs10232372	AC005154.6	cis	lung	GTEx
rs10232372	AC005154.6	cis	Artery Tibial	GTEx
rs10232372	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs10232372	AC005154.6	cis	Esophagus Mucosa	GTEx
rs10232372	LOC222159	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30591200-30633400	Weak transcription	Psoas Muscle	Psoas
2	chr7:30597400-30633200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:30601800-30633000	Weak transcription	Hela-S3	cervix
4	chr7:30603200-30628400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:30605600-30628200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:30607000-30633400	Weak transcription	Fetal Kidney	kidney
7	chr7:30612800-30628600	Weak transcription	Stomach Mucosa	stomach
8	chr7:30614000-30633200	Weak transcription	HUVEC	blood vessel
9	chr7:30615600-30633200	Weak transcription	Brain Germinal Matrix	brain
10	chr7:30615600-30633400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:30616200-30627800	Strong transcription	Primary T cells from cord blood	blood
12	chr7:30618000-30633400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:30618000-30633400	Weak transcription	Esophagus	oesophagus
14	chr7:30618400-30633400	Weak transcription	Fetal Brain Male	brain
15	chr7:30618800-30633400	Weak transcription	Brain Substantia Nigra	brain
16	chr7:30618800-30633400	Weak transcription	Colonic Mucosa	Colon
17	chr7:30619200-30632400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr7:30619200-30633200	Weak transcription	NHLF	lung
19	chr7:30619200-30633400	Weak transcription	Small Intestine	intestine
20	chr7:30620600-30633400	Weak transcription	Pancreas	Pancrea
21	chr7:30621000-30628000	Strong transcription	Primary B cells from cord blood	blood
22	chr7:30622600-30633400	Weak transcription	NH-A	brain
23	chr7:30623200-30633200	Weak transcription	A549	lung
24	chr7:30624200-30632000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr7:30624200-30633400	Weak transcription	NHDF-Ad	bronchial
26	chr7:30624600-30627800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr7:30624800-30628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr7:30624800-30628600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr7:30624800-30631400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr7:30624800-30632000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:30624800-30632000	Weak transcription	Brain Anterior Caudate	brain
32	chr7:30624800-30632200	Weak transcription	HepG2	liver
33	chr7:30624800-30633200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr7:30624800-30633200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:30624800-30633200	Weak transcription	HMEC	breast
36	chr7:30624800-30633200	Weak transcription	HSMM	muscle
37	chr7:30624800-30633200	Weak transcription	K562	blood
38	chr7:30624800-30633200	Weak transcription	NHEK	skin
39	chr7:30624800-30633400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr7:30624800-30633400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr7:30624800-30633400	Weak transcription	Aorta	Aorta
42	chr7:30624800-30633400	Weak transcription	Brain Angular Gyrus	brain
43	chr7:30624800-30633400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr7:30624800-30633400	Weak transcription	Right Ventricle	heart
45	chr7:30625000-30629800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr7:30625000-30633200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr7:30625000-30633200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr7:30625000-30633200	Weak transcription	Fetal Brain Female	brain
49	chr7:30625000-30633200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr7:30625000-30633400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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