Variant report

Variant	rs904166
Chromosome Location	chr2:47448865-47448866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr2:47448856-47449631	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47399756..47406251-chr2:47447036..47455846,12	MCF-7	breast:
2	chr2:47447257..47450209-chr2:47450575..47452374,2	K562	blood:
3	chr2:47395269..47398223-chr2:47446895..47449256,2	K562	blood:
4	chr2:47447242..47450213-chr2:47497234..47499703,2	MCF-7	breast:
5	chr2:47399705..47406684-chr2:47448496..47456698,16	K562	blood:
6	chr2:47441089..47444916-chr2:47445519..47450272,4	K562	blood:
7	chr2:47399370..47405628-chr2:47444779..47450395,9	K562	blood:
8	chr2:47448703..47450550-chr2:47457883..47459874,2	K562	blood:
9	chr2:47443128..47444876-chr2:47447324..47449483,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226087	TF binding region
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1021609	0.84[EUR][1000 genomes]
rs1021610	0.83[EUR][1000 genomes]
rs1039162	0.82[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11899830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11899833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12612040	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13391158	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13422681	0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs13430277	0.85[GIH][hapmap]
rs17485833	0.82[CEU][hapmap];0.94[MEX][hapmap];0.82[EUR][1000 genomes]
rs1874668	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1874669	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2132923	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2132924	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35551949	0.90[ASN][1000 genomes]
rs4952876	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4952877	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4953477	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4953478	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4953479	0.82[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6544972	0.95[CEU][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6721098	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67882902	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7575670	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs904167	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[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	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
3	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
5	esv10649	chr2:47429316-47472670	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs904166	C2orf61	cis	cerebellum	SCAN
rs904166	CALM2	cis	parietal	SCAN
rs904166	EPCAM	cis	cerebellum	SCAN
rs904166	THADA	cis	cerebellum	SCAN
rs904166	CALM2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47438000-47452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:47442200-47452400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:47442600-47452800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:47442800-47450200	Weak transcription	Fetal Heart	heart
5	chr2:47445800-47451000	Weak transcription	Placenta	Placenta
6	chr2:47445800-47452800	Weak transcription	Fetal Kidney	kidney
7	chr2:47446800-47449000	Weak transcription	K562	blood
8	chr2:47446800-47451600	Weak transcription	Colonic Mucosa	Colon
9	chr2:47446800-47452200	Weak transcription	Small Intestine	intestine
10	chr2:47447200-47455400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:47447400-47452200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:47447400-47452400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:47447600-47449400	Enhancers	Osteobl	bone
14	chr2:47447600-47452200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:47447600-47452400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:47447600-47452400	Enhancers	HSMM	muscle
17	chr2:47447600-47452400	Enhancers	HSMMtube	muscle
18	chr2:47447600-47455000	Enhancers	NHLF	lung
19	chr2:47448000-47449000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:47448000-47455400	Enhancers	Fetal Muscle Leg	muscle
21	chr2:47448200-47449000	Flanking Active TSS	NH-A	brain
22	chr2:47448200-47449400	Enhancers	NHDF-Ad	bronchial
23	chr2:47448200-47450200	Weak transcription	Liver	Liver
24	chr2:47448400-47450000	Weak transcription	Fetal Intestine Small	intestine
25	chr2:47448400-47450200	Weak transcription	Fetal Intestine Large	intestine
26	chr2:47448400-47450800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:47448400-47452400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:47448600-47449600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:47448800-47449400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:47448800-47449600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:47448800-47450800	Enhancers	Rectal Smooth Muscle	rectum
32	chr2:47448800-47454200	Enhancers	Colon Smooth Muscle	Colon

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