Variant report

Variant	rs12612040
Chromosome Location	chr2:47451828-47451829
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47399756..47406251-chr2:47447036..47455846,12	MCF-7	breast:
2	chr2:47451335..47453658-chr2:47453697..47456326,2	MCF-7	breast:
3	chr2:47399705..47406684-chr2:47448496..47456698,16	K562	blood:
4	chr2:47450260..47451975-chr2:47459520..47461671,2	MCF-7	breast:
5	chr2:47447257..47450209-chr2:47450575..47452374,2	K562	blood:
6	chr2:47450042..47452844-chr2:47571562..47573553,2	MCF-7	breast:
7	chr2:47399705..47405092-chr2:47450546..47458227,19	K562	blood:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction
ENSG00000226087	Chromatin interaction
ENSG00000119888	Chromatin interaction
ENSG00000234690	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10169873	0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1021609	0.82[EUR][1000 genomes]
rs1021610	0.83[EUR][1000 genomes]
rs1039162	0.83[CEU][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11899830	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11899833	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];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13422681	0.85[JPT][hapmap]
rs17485833	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]
rs1874668	0.81[AMR][1000 genomes]
rs2132924	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35911616	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4952877	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4953479	0.83[CEU][hapmap];0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6544972	0.95[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7586186	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs904166	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs904167	0.83[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][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:57 , 50 per page) page: 1 2

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	chr2:47445800-47452800	Weak transcription	Fetal Kidney	kidney
5	chr2:47446800-47452200	Weak transcription	Small Intestine	intestine
6	chr2:47447200-47455400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:47447400-47452200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:47447400-47452400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:47447600-47452200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr2:47447600-47452400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:47447600-47452400	Enhancers	HSMM	muscle
12	chr2:47447600-47452400	Enhancers	HSMMtube	muscle
13	chr2:47447600-47455000	Enhancers	NHLF	lung
14	chr2:47448000-47455400	Enhancers	Fetal Muscle Leg	muscle
15	chr2:47448400-47452400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:47448800-47454200	Enhancers	Colon Smooth Muscle	Colon
17	chr2:47449200-47452400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:47449400-47452400	Weak transcription	Brain Germinal Matrix	brain
19	chr2:47449400-47452400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:47449400-47452400	Weak transcription	Lung	lung
21	chr2:47449400-47452600	Weak transcription	Brain Substantia Nigra	brain
22	chr2:47449400-47452800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:47449400-47453000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:47449600-47452200	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:47449600-47452400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:47449600-47452400	Weak transcription	HMEC	breast
27	chr2:47449600-47452800	Weak transcription	Brain Anterior Caudate	brain
28	chr2:47449600-47453600	Enhancers	Fetal Muscle Trunk	muscle
29	chr2:47450000-47454000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:47450000-47455600	Enhancers	Fetal Intestine Small	intestine
31	chr2:47450000-47455800	Enhancers	K562	blood
32	chr2:47450000-47456000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:47450200-47452800	Enhancers	Fetal Heart	heart
34	chr2:47450200-47453600	Enhancers	Osteobl	bone
35	chr2:47450200-47454600	Enhancers	Liver	Liver
36	chr2:47450200-47455600	Enhancers	Fetal Intestine Large	intestine
37	chr2:47450400-47452600	Weak transcription	Fetal Stomach	stomach
38	chr2:47450400-47453600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:47450600-47454000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:47450800-47452400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:47450800-47452800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:47450800-47454200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:47451000-47452200	Enhancers	HepG2	liver
44	chr2:47451000-47453800	Enhancers	HUVEC	blood vessel
45	chr2:47451000-47455600	Enhancers	Placenta	Placenta
46	chr2:47451200-47454000	Enhancers	NHDF-Ad	bronchial
47	chr2:47451400-47452400	Enhancers	A549	lung
48	chr2:47451600-47452400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr2:47451600-47452800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr2:47451600-47453400	Enhancers	Colonic Mucosa	Colon

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