Variant report

Variant	rs17485833
Chromosome Location	chr2:47446888-47446889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47401550..47405628-chr2:47444779..47447737,6	K562	blood:
2	chr2:47441089..47444916-chr2:47445519..47450272,4	K562	blood:
3	chr2:47399370..47405628-chr2:47444779..47450395,9	K562	blood:
4	chr2:47436954..47438640-chr2:47446066..47448832,2	MCF-7	breast:
5	chr2:47445836..47447608-chr2:47451153..47453104,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPCAM-5	chr2:47445239-47448487	NONHSAT070552

Variant related genes	Relation type
ENSG00000226087	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10169873	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1021610	0.81[EUR][1000 genomes]
rs1039162	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11899830	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11899833	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12612040	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391158	0.82[CEU][hapmap];0.94[MEX][hapmap];0.82[EUR][1000 genomes]
rs13422681	0.85[ASW][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap]
rs1874668	0.82[AMR][1000 genomes]
rs1874669	0.81[AMR][1000 genomes]
rs2132924	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35911616	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4952877	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs4953479	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6544972	1.00[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7586186	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs904166	0.82[CEU][hapmap];0.94[MEX][hapmap];0.82[EUR][1000 genomes]
rs904167	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17485833	CALM2	cis	cerebellum	SCAN
rs17485833	THADA	cis	cerebellum	SCAN
rs17485833	EPCAM	cis	cerebellum	SCAN
rs17485833	CALM2	cis	parietal	SCAN
rs17485833	SRBD1	cis	parietal	SCAN
rs17485833	C2orf61	cis	cerebellum	SCAN
rs17485833	TTC7A	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47431400-47447200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:47438000-47452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:47442000-47448400	Enhancers	Fetal Intestine Large	intestine
4	chr2:47442200-47447200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:47442200-47448400	Enhancers	Fetal Intestine Small	intestine
6	chr2:47442200-47452400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:47442600-47447200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:47442600-47448200	Enhancers	Liver	Liver
9	chr2:47442600-47452800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:47442800-47450200	Weak transcription	Fetal Heart	heart
11	chr2:47443800-47448000	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:47444800-47447600	Weak transcription	NHLF	lung
13	chr2:47444800-47448400	Weak transcription	Hela-S3	cervix
14	chr2:47445200-47447000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr2:47445600-47447000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr2:47445800-47447400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr2:47445800-47447600	Bivalent Enhancer	HepG2	liver
18	chr2:47445800-47451000	Weak transcription	Placenta	Placenta
19	chr2:47445800-47452800	Weak transcription	Fetal Kidney	kidney
20	chr2:47446000-47447600	Enhancers	Duodenum Mucosa	Duodenum
21	chr2:47446000-47448200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:47446200-47447800	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:47446400-47448000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:47446600-47447200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:47446800-47449000	Weak transcription	K562	blood
26	chr2:47446800-47451600	Weak transcription	Colonic Mucosa	Colon
27	chr2:47446800-47452200	Weak transcription	Small Intestine	intestine

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