Variant report

Variant	rs686604
Chromosome Location	chr9:98802440-98802441
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98800966..98802558-chr9:98803277..98805259,2	MCF-7	breast:
2	chr9:98769174..98772045-chr9:98801807..98803378,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10739787	0.81[CEU][hapmap]
rs1410783	0.81[CEU][hapmap]
rs1627425	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1628930	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2296857	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs238	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs667018	0.81[CEU][hapmap]
rs683829	0.81[CEU][hapmap]
rs689980	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690575	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7023522	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs7865593	0.81[JPT][hapmap]
rs913408	0.85[YRI][hapmap]

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	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv524266	chr9:98780606-98804274	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1809137	chr9:98798752-98823646	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs686604	LINC00476	cis	Nerve Tibial	GTEx
rs686604	LINC00476	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98790800-98810800	Weak transcription	Brain Angular Gyrus	brain
2	chr9:98793600-98804600	Weak transcription	Fetal Heart	heart
3	chr9:98799200-98804600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:98801400-98809600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:98801600-98803200	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:98801600-98804200	Enhancers	Pancreas	Pancrea
7	chr9:98801600-98805400	Enhancers	Fetal Lung	lung
8	chr9:98801600-98809800	Weak transcription	Brain Hippocampus Middle	brain
9	chr9:98801800-98803400	Weak transcription	HSMMtube	muscle
10	chr9:98801800-98805400	Enhancers	Fetal Stomach	stomach
11	chr9:98801800-98809800	Weak transcription	Brain Substantia Nigra	brain
12	chr9:98801800-98810200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:98802000-98802600	Enhancers	Stomach Smooth Muscle	stomach
14	chr9:98802000-98803000	Enhancers	Esophagus	oesophagus
15	chr9:98802000-98803600	Enhancers	Gastric	stomach
16	chr9:98802000-98804800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:98802200-98802600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:98802400-98802600	Enhancers	A549	lung
19	chr9:98802400-98802800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:98802400-98802800	Bivalent Enhancer	Stomach Mucosa	stomach
21	chr9:98802400-98803200	Enhancers	Colon Smooth Muscle	Colon
22	chr9:98802400-98803400	Enhancers	Colonic Mucosa	Colon
23	chr9:98802400-98803600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:98802400-98803600	Enhancers	Fetal Intestine Small	intestine
25	chr9:98802400-98803800	Bivalent Enhancer	Placenta	Placenta
26	chr9:98802400-98806200	Weak transcription	Spleen	Spleen

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