Variant report

Variant	rs11899830
Chromosome Location	chr2:47447511-47447512
allele	G/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:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 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	chr2:47401550..47405628-chr2:47444779..47447737,6	K562	blood:
6	chr2:47441089..47444916-chr2:47445519..47450272,4	K562	blood:
7	chr2:47399370..47405628-chr2:47444779..47450395,9	K562	blood:
8	chr2:47436954..47438640-chr2:47446066..47448832,2	MCF-7	breast:
9	chr2:47443128..47444876-chr2:47447324..47449483,2	MCF-7	breast:
10	chr2:47445836..47447608-chr2:47451153..47453104,2	K562	blood:

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

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

No data

Variant related genes	Relation type
ENSG00000226087	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1021609	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1021610	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1039162	0.83[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11899833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12612040	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13391158	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13422681	0.81[ASN][1000 genomes]
rs17485833	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1874668	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1874669	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2132923	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2132924	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35551949	0.88[ASN][1000 genomes]
rs35911616	0.82[AMR][1000 genomes]
rs4952876	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4952877	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4953477	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4953478	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4953479	0.83[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61371951	0.82[AMR][1000 genomes]
rs6544972	0.95[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6721098	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67882902	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7575670	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs904166	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]
rs904167	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[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

No data

Chromatin state (count:27 , 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	chr2:47442000-47448400	Enhancers	Fetal Intestine Large	intestine
3	chr2:47442200-47448400	Enhancers	Fetal Intestine Small	intestine
4	chr2:47442200-47452400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:47442600-47448200	Enhancers	Liver	Liver
6	chr2:47442600-47452800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:47442800-47450200	Weak transcription	Fetal Heart	heart
8	chr2:47443800-47448000	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:47444800-47447600	Weak transcription	NHLF	lung
10	chr2:47444800-47448400	Weak transcription	Hela-S3	cervix
11	chr2:47445800-47447600	Bivalent Enhancer	HepG2	liver
12	chr2:47445800-47451000	Weak transcription	Placenta	Placenta
13	chr2:47445800-47452800	Weak transcription	Fetal Kidney	kidney
14	chr2:47446000-47447600	Enhancers	Duodenum Mucosa	Duodenum
15	chr2:47446000-47448200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:47446200-47447800	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:47446400-47448000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:47446800-47449000	Weak transcription	K562	blood
19	chr2:47446800-47451600	Weak transcription	Colonic Mucosa	Colon
20	chr2:47446800-47452200	Weak transcription	Small Intestine	intestine
21	chr2:47447000-47447600	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr2:47447200-47448400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr2:47447200-47448400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:47447200-47455400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:47447400-47448800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:47447400-47452200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:47447400-47452400	Weak transcription	Rectal Mucosa Donor 31	rectum

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