Variant report

Variant	rs12539597
Chromosome Location	chr7:21909867-21909868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10254159	0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs10254192	0.93[CEU][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs10485987	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs11773744	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12700317	0.82[MEX][hapmap];0.84[AMR][1000 genomes]
rs35161061	0.82[EUR][1000 genomes]
rs4722067	0.85[EUR][1000 genomes]
rs757132	0.85[CHB][hapmap];0.81[CHD][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	nsv1018133	chr7:21740118-22055283	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv830922	chr7:21793386-21964675	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12539597	IL6	cis	cerebellum	SCAN
rs12539597	CDCA7L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21904600-21910400	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr7:21904600-21910600	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr7:21905000-21910000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr7:21905000-21910200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:21905000-21910800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr7:21905200-21910000	Enhancers	H9 Cell Line	embryonic stem cell
7	chr7:21905200-21910200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr7:21905600-21916200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:21905800-21916200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:21906400-21910200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr7:21906600-21910600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:21906600-21916200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:21906800-21916200	Weak transcription	Primary B cells from cord blood	blood
14	chr7:21906800-21916200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:21907000-21910000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:21907200-21910200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:21907400-21916000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr7:21907400-21937200	Weak transcription	Fetal Thymus	thymus
19	chr7:21907800-21910200	Enhancers	Fetal Heart	heart
20	chr7:21907800-21916200	Weak transcription	Thymus	Thymus
21	chr7:21908000-21910200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr7:21908000-21910400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr7:21908400-21910200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr7:21908400-21936600	Weak transcription	Primary T cells from cord blood	blood
25	chr7:21908600-21910200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr7:21908800-21910600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr7:21908800-21916200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:21908800-21916200	Weak transcription	Fetal Intestine Small	intestine
29	chr7:21908800-21921200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:21909000-21910000	Enhancers	Left Ventricle	heart
31	chr7:21909200-21910200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:21909200-21913600	Weak transcription	Gastric	stomach
33	chr7:21909400-21910000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr7:21909400-21910000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:21909400-21910000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:21909400-21910000	Enhancers	Right Atrium	heart
37	chr7:21909600-21910000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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