Variant report

Variant	rs904167
Chromosome Location	chr2:47449545-47449546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:47449015-47449591	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr2:47449043-47449547	SK-N-SH	brain:	n/a	n/a
3	MAX	chr2:47448994-47449593	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr2:47449054-47449579	ECC-1	luminal epithelium:	n/a	n/a
5	NFIC	chr2:47448919-47449653	SK-N-SH	brain:	n/a	n/a
6	NFIC	chr2:47448856-47449631	ECC-1	luminal epithelium:	n/a	n/a
7	NFIC	chr2:47448984-47449611	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:8 , 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	chr2:47447242..47450213-chr2:47497234..47499703,2	MCF-7	breast:
4	chr2:47399705..47406684-chr2:47448496..47456698,16	K562	blood:
5	chr2:47441089..47444916-chr2:47445519..47450272,4	K562	blood:
6	chr2:47399370..47405628-chr2:47444779..47450395,9	K562	blood:
7	chr2:47448703..47450550-chr2:47457883..47459874,2	K562	blood:
8	chr2:47449135..47451473-chr2:47453738..47455676,2	MCF-7	breast:

No data

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

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10169873	0.84[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1039162	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11899830	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]
rs11899833	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]
rs12612040	0.83[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13391158	0.82[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13422681	0.81[ASN][1000 genomes]
rs17485833	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1874668	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1874669	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2132923	0.80[EUR][1000 genomes]
rs2132924	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35551949	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35911616	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4952876	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4952877	0.83[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4953477	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4953478	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4953479	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6544972	0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6721098	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67882902	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7575670	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7586186	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs904166	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:4 , 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	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
4	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:46 , 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	chr2:47446800-47451600	Weak transcription	Colonic Mucosa	Colon
8	chr2:47446800-47452200	Weak transcription	Small Intestine	intestine
9	chr2:47447200-47455400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:47447400-47452200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:47447400-47452400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:47447600-47452200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:47447600-47452400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:47447600-47452400	Enhancers	HSMM	muscle
15	chr2:47447600-47452400	Enhancers	HSMMtube	muscle
16	chr2:47447600-47455000	Enhancers	NHLF	lung
17	chr2:47448000-47455400	Enhancers	Fetal Muscle Leg	muscle
18	chr2:47448200-47450200	Weak transcription	Liver	Liver
19	chr2:47448400-47450000	Weak transcription	Fetal Intestine Small	intestine
20	chr2:47448400-47450200	Weak transcription	Fetal Intestine Large	intestine
21	chr2:47448400-47450800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:47448400-47452400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:47448600-47449600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:47448800-47449600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr2:47448800-47450800	Enhancers	Rectal Smooth Muscle	rectum
26	chr2:47448800-47454200	Enhancers	Colon Smooth Muscle	Colon
27	chr2:47449000-47449600	Enhancers	Brain Anterior Caudate	brain
28	chr2:47449000-47449600	Enhancers	Brain Hippocampus Middle	brain
29	chr2:47449000-47449600	Enhancers	K562	blood
30	chr2:47449000-47449600	Enhancers	NH-A	brain
31	chr2:47449200-47449600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:47449200-47449600	Enhancers	HMEC	breast
33	chr2:47449200-47450400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr2:47449200-47452400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:47449400-47450200	Weak transcription	Osteobl	bone
36	chr2:47449400-47450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:47449400-47451000	Weak transcription	HUVEC	blood vessel
38	chr2:47449400-47451200	Weak transcription	NHDF-Ad	bronchial
39	chr2:47449400-47451600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:47449400-47451600	Weak transcription	Psoas Muscle	Psoas
41	chr2:47449400-47452400	Weak transcription	Brain Germinal Matrix	brain
42	chr2:47449400-47452400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:47449400-47452400	Weak transcription	Lung	lung
44	chr2:47449400-47452600	Weak transcription	Brain Substantia Nigra	brain
45	chr2:47449400-47452800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:47449400-47453000	Weak transcription	Brain Cingulate Gyrus	brain

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