Variant report

Variant	rs2236746
Chromosome Location	chr12:49691567-49691568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49691260..49692031-chr12:49752077..49752849,2	MCF-7	breast:
2	chr12:49689988..49692308-chr12:49713640..49717456,5	K562	blood:
3	chr12:49691342..49692923-chr12:49735601..49736627,8	MCF-7	breast:
4	chr12:49686580..49692358-chr12:49712251..49718367,13	MCF-7	breast:
5	chr12:49691489..49693674-chr12:49738441..49740198,2	MCF-7	breast:
6	chr12:49524142..49526154-chr12:49690463..49692891,2	MCF-7	breast:
7	chr12:49656941..49662685-chr12:49687034..49693573,13	MCF-7	breast:
8	chr12:49685493..49694205-chr12:49728829..49734805,16	K562	blood:
9	chr12:49664091..49667882-chr12:49690109..49694759,4	K562	blood:
10	chr12:49666275..49670972-chr12:49688443..49691988,7	K562	blood:
11	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
12	chr12:49691061..49691606-chr12:49735920..49736671,2	K562	blood:
13	chr12:49689044..49692243-chr12:49760659..49764012,4	MCF-7	breast:
14	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
15	chr12:49691373..49692810-chr12:49735826..49736936,11	MCF-7	breast:
16	chr12:49657190..49661099-chr12:49688432..49694179,9	K562	blood:
17	chr12:49654800..49660850-chr12:49685742..49692441,19	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258017	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000258101	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10506284	1.00[CHB][hapmap]
rs10875946	1.00[ASN][1000 genomes]
rs10875948	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11168967	0.87[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168970	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168971	1.00[ASN][1000 genomes]
rs11168972	1.00[ASN][1000 genomes]
rs11168973	0.93[CEU][hapmap]
rs11168975	1.00[JPT][hapmap]
rs11169016	1.00[CHB][hapmap]
rs11834161	1.00[CHB][hapmap]
rs11835037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835303	1.00[JPT][hapmap]
rs11837234	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12301545	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301632	1.00[CHB][hapmap]
rs12304800	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306118	1.00[CHB][hapmap]
rs12313435	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315095	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315130	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315996	1.00[CHB][hapmap]
rs12317532	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12318618	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12322335	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322783	0.93[CEU][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs12322798	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580931	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs12581343	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12581428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2070760	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2070761	1.00[ASN][1000 genomes]
rs2230550	0.93[ASN][1000 genomes]
rs2272478	1.00[CHB][hapmap]
rs28493849	0.84[EUR][1000 genomes]
rs28543370	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28798494	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28808573	0.83[AMR][1000 genomes]
rs28823960	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28857010	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088008	1.00[JPT][hapmap]
rs34791911	1.00[ASN][1000 genomes]
rs3847764	1.00[CHB][hapmap]
rs3898446	1.00[ASN][1000 genomes]
rs4243545	1.00[JPT][hapmap]
rs4898516	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4898517	1.00[ASN][1000 genomes]
rs4898519	1.00[JPT][hapmap]
rs57451017	1.00[ASN][1000 genomes]
rs57755392	1.00[ASN][1000 genomes]
rs60174686	0.82[ASN][1000 genomes]
rs61023481	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61455481	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580707	1.00[CHB][hapmap]
rs6580709	1.00[CHB][hapmap]
rs6580716	1.00[CHB][hapmap]
rs67309388	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7136538	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136945	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139061	1.00[CHB][hapmap]
rs7294648	1.00[CHB][hapmap]
rs7294873	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294973	1.00[CHB][hapmap]
rs7295162	1.00[CHB][hapmap]
rs7295247	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309997	1.00[CHB][hapmap]
rs73112143	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7342318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342365	1.00[CHB][hapmap]
rs7342370	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7398252	1.00[ASN][1000 genomes]
rs7955541	1.00[CHB][hapmap]
rs7962951	1.00[CHB][hapmap]
rs7969099	1.00[CHB][hapmap]
rs7975431	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976165	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv558834	chr12:49676010-49691567	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
8	nsv826367	chr12:49686493-49691709	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2236746	MCRS1	cis	cerebellum	SCAN
rs2236746	CXorf26	trans	cerebellum	SCAN
rs2236746	PRPH	cis	cerebellum	SCAN
rs2236746	TMEM117	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49686600-49692000	Bivalent Enhancer	Placenta	Placenta
2	chr12:49687800-49692000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr12:49688600-49691800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr12:49689600-49692600	Bivalent Enhancer	Stomach Mucosa	stomach
5	chr12:49689800-49691800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:49690200-49691600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:49690200-49692000	Bivalent Enhancer	Fetal Thymus	thymus
8	chr12:49690400-49691600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr12:49690400-49691600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
10	chr12:49690400-49691600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:49690400-49691600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr12:49690400-49691800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:49690600-49691600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:49690600-49691600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:49690600-49691600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:49690600-49691600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
17	chr12:49690600-49691600	Bivalent Enhancer	Small Intestine	intestine
18	chr12:49690600-49691800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr12:49690600-49691800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr12:49690800-49691800	Enhancers	Spleen	Spleen
21	chr12:49690800-49692000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:49690800-49692000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr12:49690800-49692000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
24	chr12:49691000-49691600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr12:49691000-49691600	Bivalent Enhancer	Primary B cells from cord blood	blood
26	chr12:49691000-49691600	Bivalent Enhancer	Fetal Stomach	stomach
27	chr12:49691000-49691600	Active TSS	Right Atrium	heart
28	chr12:49691000-49691600	Active TSS	A549	lung
29	chr12:49691000-49691600	Active TSS	Hela-S3	cervix
30	chr12:49691000-49691800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
31	chr12:49691000-49692000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:49691200-49691600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr12:49691200-49691600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
34	chr12:49691200-49691600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:49691200-49691600	Bivalent Enhancer	Adipose Nuclei	Adipose
36	chr12:49691200-49691600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
37	chr12:49691200-49691600	Enhancers	Pancreas	Pancrea
38	chr12:49691200-49691600	Bivalent/Poised TSS	Thymus	Thymus
39	chr12:49691200-49691600	Active TSS	K562	blood
40	chr12:49691200-49691800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:49691200-49691800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr12:49691200-49691800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
43	chr12:49691200-49691800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
44	chr12:49691200-49691800	Bivalent Enhancer	Esophagus	oesophagus
45	chr12:49691200-49691800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr12:49691200-49691800	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr12:49691200-49692000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
48	chr12:49691200-49692000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
49	chr12:49691200-49692000	Bivalent Enhancer	Fetal Intestine Large	intestine
50	chr12:49691200-49692200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell

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