Variant report

Variant	rs12349495
Chromosome Location	chr9:116026982-116026983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116023106..116028620-chr9:116032404..116039334,10	MCF-7	breast:
2	chr9:116025697..116028856-chr9:116035797..116038156,5	K562	blood:
3	chr9:116021697..116024612-chr9:116025730..116027476,2	MCF-7	breast:
4	chr9:116025855..116027571-chr9:116035430..116037680,2	MCF-7	breast:
5	chr9:116011649..116014033-chr9:116026530..116028582,2	K562	blood:
6	chr9:116024711..116027399-chr9:116031082..116034074,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176386	Chromatin interaction
ENSG00000136875	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10759634	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10817463	0.83[ASN][1000 genomes]
rs10817464	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10817466	0.83[ASN][1000 genomes]
rs10817469	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10817471	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10817472	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10981690	0.80[EUR][1000 genomes]
rs10981695	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10981705	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12336832	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341669	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12342197	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12342549	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12343330	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348629	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12349500	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12349614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351168	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12351630	0.87[ASN][1000 genomes]
rs12352784	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12352925	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17831256	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28733164	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58402825	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66509679	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72758255	0.84[EUR][1000 genomes]
rs7858741	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7863910	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115996000-116031600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:116008200-116037000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:116009600-116029800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:116010200-116031800	Weak transcription	Fetal Heart	heart
5	chr9:116011400-116028800	Weak transcription	Fetal Kidney	kidney
6	chr9:116017600-116031800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr9:116018000-116027600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:116018600-116036000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr9:116019200-116028800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr9:116019600-116033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr9:116020000-116029600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr9:116020600-116027400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr9:116020600-116031600	Weak transcription	HUVEC	blood vessel
14	chr9:116021000-116036000	Strong transcription	Fetal Stomach	stomach
15	chr9:116021200-116031600	Weak transcription	Fetal Brain Male	brain
16	chr9:116021200-116032200	Weak transcription	Small Intestine	intestine
17	chr9:116021200-116032600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:116021400-116029800	Weak transcription	Primary B cells from cord blood	blood
19	chr9:116021400-116032200	Weak transcription	Pancreas	Pancrea
20	chr9:116022400-116036600	Weak transcription	Stomach Mucosa	stomach
21	chr9:116022600-116028600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr9:116022600-116029400	Weak transcription	NH-A	brain
23	chr9:116022600-116031600	Weak transcription	NHDF-Ad	bronchial
24	chr9:116022800-116027200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr9:116022800-116028600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr9:116022800-116028600	Weak transcription	Fetal Thymus	thymus
27	chr9:116022800-116029000	Weak transcription	A549	lung
28	chr9:116022800-116030200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr9:116022800-116030600	Weak transcription	K562	blood
30	chr9:116022800-116031600	Weak transcription	Psoas Muscle	Psoas
31	chr9:116022800-116031800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:116022800-116032200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:116022800-116032200	Weak transcription	Esophagus	oesophagus
34	chr9:116022800-116036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr9:116023000-116027200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:116023000-116027200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr9:116023000-116027400	Weak transcription	Dnd41	blood
38	chr9:116023000-116028400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr9:116023000-116028600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr9:116023000-116028600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:116023000-116029800	Weak transcription	Thymus	Thymus
42	chr9:116023000-116029800	Weak transcription	Spleen	Spleen
43	chr9:116023000-116031400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr9:116023000-116031800	Weak transcription	NHLF	lung
45	chr9:116023000-116032200	Weak transcription	Gastric	stomach
46	chr9:116023000-116033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:116023000-116033200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:116023000-116036800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr9:116023200-116027800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr9:116023200-116028400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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