Variant report

Variant	rs2296857
Chromosome Location	chr9:98803415-98803416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98800086..98802107-chr9:98802951..98805065,2	K562	blood:
2	chr9:98800966..98802558-chr9:98803277..98805259,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10760692	0.84[GIH][hapmap]
rs12004422	0.81[GIH][hapmap]
rs1627425	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1628930	0.84[EUR][1000 genomes]
rs238	1.00[ASW][hapmap];0.84[GIH][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs583716	0.84[GIH][hapmap]
rs601916	0.84[GIH][hapmap]
rs643815	0.84[GIH][hapmap]
rs6479036	0.84[GIH][hapmap]
rs680468	0.86[GIH][hapmap]
rs680754	0.84[GIH][hapmap]
rs686604	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689871	0.84[GIH][hapmap]
rs689979	0.84[GIH][hapmap]
rs689980	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs690455	0.84[GIH][hapmap]
rs690484	0.84[GIH][hapmap]
rs690575	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7023522	0.86[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs7024710	0.84[GIH][hapmap]
rs913408	0.84[GIH][hapmap];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
rs2296857	LINC00476	cis	Adipose Subcutaneous	GTEx
rs2296857	LINC00476	cis	Nerve Tibial	GTEx

Chromatin state (count:40 , 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	chr9:98801600-98804200	Enhancers	Pancreas	Pancrea
6	chr9:98801600-98805400	Enhancers	Fetal Lung	lung
7	chr9:98801600-98809800	Weak transcription	Brain Hippocampus Middle	brain
8	chr9:98801800-98805400	Enhancers	Fetal Stomach	stomach
9	chr9:98801800-98809800	Weak transcription	Brain Substantia Nigra	brain
10	chr9:98801800-98810200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:98802000-98803600	Enhancers	Gastric	stomach
12	chr9:98802000-98804800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:98802400-98803600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:98802400-98803600	Enhancers	Fetal Intestine Small	intestine
15	chr9:98802400-98803800	Bivalent Enhancer	Placenta	Placenta
16	chr9:98802400-98806200	Weak transcription	Spleen	Spleen
17	chr9:98802600-98803600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
18	chr9:98802600-98803600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr9:98802600-98803600	Enhancers	Fetal Intestine Large	intestine
20	chr9:98802600-98803600	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr9:98802600-98803800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr9:98802600-98803800	Enhancers	Lung	lung
23	chr9:98802600-98804000	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr9:98802800-98803600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:98802800-98803600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
26	chr9:98802800-98803600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:98802800-98803800	Enhancers	Fetal Muscle Trunk	muscle
28	chr9:98802800-98803800	Enhancers	Ovary	ovary
29	chr9:98802800-98803800	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr9:98803000-98803600	Enhancers	Small Intestine	intestine
31	chr9:98803000-98803600	Flanking Active TSS	HepG2	liver
32	chr9:98803000-98804000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:98803000-98804400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:98803000-98804400	Bivalent Enhancer	Stomach Mucosa	stomach
35	chr9:98803000-98808600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:98803000-98810200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:98803200-98803600	Active TSS	A549	lung
38	chr9:98803200-98805200	Enhancers	Fetal Muscle Leg	muscle
39	chr9:98803400-98804000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:98803400-98807200	Enhancers	HSMMtube	muscle

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