Variant report

Variant	rs4953438
Chromosome Location	chr2:47188177-47188178
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:47187722-47188180	A549	lung:	n/a	chr2:47187947-47187961 chr2:47187946-47187965
2	POLR2A	chr2:47188138-47188195	Hela-S3	cervix:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47168340..47172583-chr2:47183123..47189203,6	MCF-7	breast:
2	chr2:47187898..47188405-chr2:47213880..47214767,2	K562	blood:
3	chr2:47187033..47189469-chr2:47193836..47195878,3	K562	blood:
4	chr2:47141694..47145106-chr2:47185858..47188947,4	MCF-7	breast:
5	chr2:47187196..47189575-chr2:47193868..47196024,2	MCF-7	breast:
6	chr2:47167518..47170357-chr2:47185466..47188388,3	K562	blood:
7	chr2:47176750..47178976-chr2:47185313..47188248,2	MCF-7	breast:
8	chr2:47180801..47184692-chr2:47184909..47188925,6	K562	blood:
9	chr2:47187193..47190243-chr2:47190337..47193752,4	MCF-7	breast:
10	chr2:47187408..47189376-chr2:47192162..47193765,2	K562	blood:
11	chr2:47181921..47184110-chr2:47186607..47189262,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272814	TF binding region
ENSG00000272814	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10183233	0.83[CHB][hapmap]
rs10495941	0.96[CEU][hapmap];1.00[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];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125103	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125104	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11125105	0.83[ASN][1000 genomes]
rs1122516	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11680492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685461	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]
rs12053441	0.83[EUR][1000 genomes]
rs12712980	1.00[CEU][hapmap];1.00[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];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712982	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12712984	0.90[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13002842	0.87[CEU][hapmap]
rs13014374	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs1865258	0.81[GIH][hapmap];0.83[LWK][hapmap]
rs1865261	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278449	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2278450	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28434195	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28694585	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4952857	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6544943	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6544944	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6713810	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6727651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6745836	0.81[EUR][1000 genomes]
rs735887	0.82[ASN][1000 genomes]
rs735888	0.81[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs7557193	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7560371	0.82[CHB][hapmap]
rs7602813	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs892380	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4953438	EPCAM	cis	parietal	SCAN
rs4953438	MCFD2	cis	parietal	SCAN

Chromatin state (count:121 , 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	chr2:47177600-47188200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:47177600-47190000	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr2:47177600-47191200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:47178400-47192800	Strong transcription	Thymus	Thymus
11	chr2:47178600-47189800	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:47178800-47189400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:47178800-47190000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:47178800-47191400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:47179000-47188200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:47179000-47191000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:47179000-47192800	Strong transcription	Primary T cells from cord blood	blood
18	chr2:47179200-47195000	Strong transcription	Fetal Thymus	thymus
19	chr2:47179400-47189600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:47179400-47191400	Strong transcription	Primary hematopoietic stem cells	blood
21	chr2:47179400-47192200	Strong transcription	Primary B cells from cord blood	blood
22	chr2:47179400-47192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:47179400-47193800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:47179800-47189400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr2:47181200-47192200	Strong transcription	GM12878-XiMat	blood
26	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:47182600-47189800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:47182600-47190400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:47182800-47188400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:47182800-47189600	Strong transcription	Fetal Muscle Leg	muscle
31	chr2:47183000-47189800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:47183000-47189800	Weak transcription	K562	blood
33	chr2:47183000-47192000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:47183000-47195000	Weak transcription	Small Intestine	intestine
35	chr2:47183200-47188200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr2:47183200-47188400	Strong transcription	Placenta	Placenta
37	chr2:47183200-47189000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:47183200-47190400	Strong transcription	Osteobl	bone
39	chr2:47183400-47188200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:47183400-47188200	Strong transcription	Brain Hippocampus Middle	brain
41	chr2:47183400-47188400	Strong transcription	Lung	lung
42	chr2:47183400-47188400	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr2:47183400-47188600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:47183400-47189200	Strong transcription	HepG2	liver
45	chr2:47183400-47191000	Strong transcription	NHLF	lung
46	chr2:47183400-47191200	Strong transcription	HSMM	muscle
47	chr2:47183400-47192200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr2:47183400-47192600	Strong transcription	Fetal Intestine Large	intestine
49	chr2:47183400-47193400	Strong transcription	Fetal Intestine Small	intestine
50	chr2:47183600-47188200	Strong transcription	NHDF-Ad	bronchial

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