Variant report

Variant	rs11685461
Chromosome Location	chr2:47190992-47190993
allele	A/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47164600..47167090-chr2:47190950..47193614,2	K562	blood:
2	chr2:47188627..47191352-chr2:48004786..48007353,2	MCF-7	breast:
3	chr2:47182825..47184577-chr2:47189939..47191603,2	K562	blood:
4	chr2:47187193..47190243-chr2:47190337..47193752,4	MCF-7	breast:
5	chr2:47166769..47171325-chr2:47189456..47193821,11	MCF-7	breast:
6	chr2:47164675..47170526-chr2:47188235..47196918,12	MCF-7	breast:
7	chr2:47183578..47186392-chr2:47190442..47192561,4	MCF-7	breast:
8	chr2:47188688..47191664-chr2:47211239..47213547,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction
ENSG00000272814	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10495941	0.94[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10779934	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs11125103	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11125104	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11125105	0.83[ASN][1000 genomes]
rs1122516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11680492	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12053441	0.82[EUR][1000 genomes]
rs12712980	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12712981	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12712982	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712983	0.81[CHB][hapmap]
rs12712984	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13002842	0.87[CEU][hapmap]
rs13014374	0.83[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs1865258	0.81[GIH][hapmap]
rs1865261	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278449	0.91[CEU][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes]
rs2278450	0.91[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28434195	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28694585	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4952857	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4953437	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953438	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6544943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6544944	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6713810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6727651	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6731862	0.84[CHB][hapmap]
rs6745836	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs735887	0.90[ASN][1000 genomes]
rs735888	0.81[CEU][hapmap];0.94[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs7557193	0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7560371	0.88[CHB][hapmap]
rs7602813	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs892380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11685461	MCFD2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
2	chr2:47173000-47191800	Weak transcription	Fetal Brain Male	brain
3	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:47176400-47192600	Strong transcription	Dnd41	blood
5	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:47177400-47192800	Strong transcription	Fetal Stomach	stomach
7	chr2:47177600-47191200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:47178400-47192800	Strong transcription	Thymus	Thymus
9	chr2:47178800-47191400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:47179000-47191000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:47179000-47192800	Strong transcription	Primary T cells from cord blood	blood
12	chr2:47179200-47195000	Strong transcription	Fetal Thymus	thymus
13	chr2:47179400-47191400	Strong transcription	Primary hematopoietic stem cells	blood
14	chr2:47179400-47192200	Strong transcription	Primary B cells from cord blood	blood
15	chr2:47179400-47192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:47179400-47193800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr2:47181200-47192200	Strong transcription	GM12878-XiMat	blood
18	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:47183000-47192000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:47183000-47195000	Weak transcription	Small Intestine	intestine
21	chr2:47183400-47191000	Strong transcription	NHLF	lung
22	chr2:47183400-47191200	Strong transcription	HSMM	muscle
23	chr2:47183400-47192200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr2:47183400-47192600	Strong transcription	Fetal Intestine Large	intestine
25	chr2:47183400-47193400	Strong transcription	Fetal Intestine Small	intestine
26	chr2:47184200-47194400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:47184600-47197600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:47184600-47205000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr2:47185000-47206000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:47185200-47210200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:47185400-47191000	Strong transcription	Stomach Smooth Muscle	stomach
32	chr2:47185400-47205800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:47185400-47210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:47185600-47195000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:47185800-47195000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:47186000-47191000	Weak transcription	Stomach Mucosa	stomach
37	chr2:47186000-47194400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:47186000-47195000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:47186000-47195000	Weak transcription	Left Ventricle	heart
40	chr2:47186200-47192000	Weak transcription	Ovary	ovary
41	chr2:47186200-47200800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:47186400-47205600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:47186600-47191400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:47186600-47194400	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:47186800-47205200	Weak transcription	Gastric	stomach
46	chr2:47186800-47205800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:47187000-47195000	Weak transcription	Right Ventricle	heart
48	chr2:47187200-47197000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:47187400-47191000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:47187400-47206000	Weak transcription	Fetal Brain Female	brain

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