Variant report

Variant	rs10215972
Chromosome Location	chr7:129586354-129586355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:129584954..129586824-chr7:129590522..129592787,2	K562	blood:
2	chr7:129583013..129586797-chr7:129588457..129590317,4	K562	blood:
3	chr7:129585963..129587755-chr7:129588456..129590565,2	MCF-7	breast:
4	chr7:129575738..129578941-chr7:129585169..129588929,4	K562	blood:

Variant related genes	Relation type
ENSG00000186591	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10253233	0.96[YRI][hapmap]
rs10500121	0.88[LWK][hapmap];0.96[YRI][hapmap]
rs1464973	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1486831	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs17162295	0.95[YRI][hapmap]
rs1725077	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2631602	0.81[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2708637	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2727464	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2727487	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2727499	0.93[JPT][hapmap]
rs2727500	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs34297290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3807120	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs3817530	0.84[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4728180	0.81[ASN][1000 genomes]
rs4731638	0.81[ASN][1000 genomes]
rs62489374	0.83[AFR][1000 genomes]
rs62489377	0.82[ASN][1000 genomes]
rs62489378	0.83[ASN][1000 genomes]
rs62489379	0.83[ASN][1000 genomes]
rs62489381	0.83[ASN][1000 genomes]
rs62491539	0.82[ASN][1000 genomes]
rs6467267	0.88[LWK][hapmap];0.91[YRI][hapmap]
rs7789191	0.84[AFR][1000 genomes]
rs7801603	0.88[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][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	nsv533849	chr7:129462947-129616625	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv831129	chr7:129525406-129702477	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10215972	SMO	cis	cerebellum	SCAN
rs10215972	C7orf45	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129530000-129587600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:129549200-129586800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:129549800-129588200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr7:129555200-129587000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr7:129556600-129588000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr7:129557400-129587000	Weak transcription	Fetal Lung	lung
7	chr7:129558000-129587600	Weak transcription	Brain Germinal Matrix	brain
8	chr7:129559600-129588000	Weak transcription	Esophagus	oesophagus
9	chr7:129559800-129588600	Weak transcription	Colonic Mucosa	Colon
10	chr7:129564400-129586800	Weak transcription	A549	lung
11	chr7:129565200-129587400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:129565400-129587400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:129565600-129586400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr7:129565600-129587600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr7:129565600-129588200	Weak transcription	HMEC	breast
16	chr7:129565800-129586600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr7:129565800-129586800	Weak transcription	Brain Anterior Caudate	brain
18	chr7:129565800-129587000	Weak transcription	NH-A	brain
19	chr7:129565800-129587400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:129565800-129587600	Weak transcription	Brain Angular Gyrus	brain
21	chr7:129565800-129588200	Weak transcription	HUVEC	blood vessel
22	chr7:129566000-129586400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr7:129566000-129586400	Weak transcription	NHDF-Ad	bronchial
24	chr7:129566000-129587000	Weak transcription	Adipose Nuclei	Adipose
25	chr7:129566000-129587000	Weak transcription	Brain Hippocampus Middle	brain
26	chr7:129566200-129586800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:129569000-129588000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:129569600-129586400	Weak transcription	Liver	Liver
29	chr7:129569800-129587800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:129570200-129587400	Weak transcription	Stomach Mucosa	stomach
31	chr7:129573200-129588200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr7:129573400-129586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:129573400-129586800	Weak transcription	NHLF	lung
34	chr7:129573400-129587400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:129573800-129586400	Weak transcription	Hela-S3	cervix
36	chr7:129573800-129588000	Weak transcription	HSMMtube	muscle
37	chr7:129573800-129588200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr7:129574000-129587000	Weak transcription	NHEK	skin
39	chr7:129574000-129587600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr7:129574000-129588600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr7:129575400-129587600	Weak transcription	Fetal Intestine Large	intestine
42	chr7:129577200-129587600	Weak transcription	Thymus	Thymus
43	chr7:129577800-129589600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr7:129578000-129586800	Weak transcription	Osteobl	bone
45	chr7:129578200-129586800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:129578400-129586800	Weak transcription	Fetal Kidney	kidney
47	chr7:129579400-129588400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:129580000-129586800	Weak transcription	Brain Substantia Nigra	brain
49	chr7:129580000-129587600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:129580600-129586600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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