Variant report

Variant	rs12072096
Chromosome Location	chr1:62523223-62523224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12070254	0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12076492	0.87[CEU][hapmap]
rs17123017	0.93[CEU][hapmap]
rs2025290	0.80[CEU][hapmap]
rs2067882	0.80[CEU][hapmap]
rs2365985	0.80[CEU][hapmap]
rs2476186	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2498979	0.85[ASN][1000 genomes]
rs3762449	0.81[CEU][hapmap]
rs41394744	0.81[CEU][hapmap]
rs4915793	0.81[CEU][hapmap]
rs56811366	0.85[ASN][1000 genomes]
rs6665231	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9436655	1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12072096	ROR1	cis	cerebellum	SCAN
rs12072096	INADL	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:62469000-62533600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:62494600-62524400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:62494600-62524400	Weak transcription	Esophagus	oesophagus
8	chr1:62495200-62544800	Weak transcription	Liver	Liver
9	chr1:62504800-62531400	Weak transcription	Aorta	Aorta
10	chr1:62507200-62523600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:62507400-62524600	Weak transcription	HepG2	liver
12	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
13	chr1:62508800-62532000	Weak transcription	Fetal Stomach	stomach
14	chr1:62511400-62531600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:62511400-62531800	Weak transcription	NHEK	skin
16	chr1:62511600-62531200	Weak transcription	Lung	lung
17	chr1:62511800-62529600	Weak transcription	Right Atrium	heart
18	chr1:62512200-62524200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:62514000-62524400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:62515400-62552400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:62516800-62524400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:62518200-62531600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:62518200-62531800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:62518800-62531600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:62518800-62532000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:62519000-62523400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:62519000-62530600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:62519000-62532000	Weak transcription	Fetal Intestine Large	intestine
29	chr1:62519000-62541600	Weak transcription	HMEC	breast
30	chr1:62519000-62550000	Weak transcription	Primary T cells from cord blood	blood
31	chr1:62519000-62550000	Weak transcription	Pancreas	Pancrea
32	chr1:62519000-62552000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:62519800-62523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:62520200-62530400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:62521800-62546200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:62522200-62527400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:62522600-62523400	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr1:62522600-62523400	Enhancers	Left Ventricle	heart
39	chr1:62522600-62523800	Enhancers	H9 Cell Line	embryonic stem cell
40	chr1:62522600-62525600	Enhancers	H1 Cell Line	embryonic stem cell
41	chr1:62522800-62523600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:62522800-62523800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr1:62522800-62524800	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr1:62522800-62525200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr1:62522800-62525600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr1:62523000-62524600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:62523000-62525000	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr1:62523200-62524400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:62523200-62524800	Enhancers	Fetal Heart	heart
50	chr1:62523200-62526000	Weak transcription	Fetal Intestine Small	intestine

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