Variant report

Variant	rs12618708
Chromosome Location	chr2:188409638-188409639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:188407472..188409911-chr2:188410680..188413536,3	MCF-7	breast:
2	chr2:188408868..188410387-chr2:188412786..188414991,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10201169	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12612748	0.89[ASN][1000 genomes]
rs12616095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12622831	0.89[ASN][1000 genomes]
rs13427934	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13432763	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861309	0.89[ASN][1000 genomes]
rs55818121	1.00[AFR][1000 genomes]
rs55822404	1.00[AFR][1000 genomes]
rs55881028	0.91[ASN][1000 genomes]
rs55933355	1.00[AFR][1000 genomes]
rs56127332	1.00[AFR][1000 genomes]
rs56401763	1.00[AFR][1000 genomes]
rs6737903	0.89[ASN][1000 genomes]
rs72904378	1.00[AFR][1000 genomes]
rs7565807	0.89[ASN][1000 genomes]
rs8176418	0.89[ASN][1000 genomes]
rs8176420	0.83[ASN][1000 genomes]
rs8176444	0.89[ASN][1000 genomes]
rs8176482	0.89[ASN][1000 genomes]
rs8176490	0.89[ASN][1000 genomes]
rs8176594	0.89[ASN][1000 genomes]
rs8176603	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875560	chr2:188219052-188508011	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv875561	chr2:188226900-188440752	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv875564	chr2:188258904-188414161	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv875565	chr2:188258904-188440752	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv875566	chr2:188258904-188626214	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv875567	chr2:188258904-188673462	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv834488	chr2:188268434-188415496	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv875568	chr2:188291105-188653806	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv875576	chr2:188343497-188482933	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv875577	chr2:188343497-188500930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv875578	chr2:188343497-188690187	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv997899	chr2:188356689-188531831	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1014298	chr2:188359747-188531831	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1013166	chr2:188359747-188544803	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv1014942	chr2:188360116-188480738	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv584038	chr2:188370232-188450136	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv875580	chr2:188370232-188521234	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	esv2757845	chr2:188380042-188503185	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	esv2759108	chr2:188380042-188503185	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv875581	chr2:188390819-188521234	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv875582	chr2:188395700-188508011	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv875583	chr2:188395700-188521234	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188392200-188413200	Weak transcription	Psoas Muscle	Psoas
2	chr2:188398400-188418000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:188404800-188410000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:188405800-188410200	Enhancers	Liver	Liver
5	chr2:188406000-188410200	Enhancers	Stomach Mucosa	stomach
6	chr2:188406200-188418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:188406600-188413600	Weak transcription	Right Atrium	heart
8	chr2:188406800-188410200	Weak transcription	Fetal Kidney	kidney
9	chr2:188406800-188410600	Weak transcription	Fetal Stomach	stomach
10	chr2:188406800-188411400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:188406800-188411600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:188406800-188411600	Weak transcription	NHEK	skin
13	chr2:188406800-188411800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:188406800-188411800	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:188406800-188411800	Weak transcription	HMEC	breast
16	chr2:188406800-188412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:188406800-188412400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:188406800-188413400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:188406800-188415600	Weak transcription	Spleen	Spleen
20	chr2:188406800-188417200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:188406800-188418000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:188406800-188418600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:188406800-188422800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:188407000-188410000	Genic enhancers	HepG2	liver
25	chr2:188407000-188410200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:188407000-188411400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:188407000-188411600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:188407000-188411800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:188407000-188414600	Weak transcription	Fetal Intestine Small	intestine
30	chr2:188407000-188414800	Weak transcription	Small Intestine	intestine
31	chr2:188407200-188410200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:188407200-188410200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:188407200-188414600	Weak transcription	Aorta	Aorta
34	chr2:188407400-188410000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:188407400-188410000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:188407400-188411800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:188408000-188409800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:188408000-188409800	Genic enhancers	HSMM	muscle
39	chr2:188408200-188409800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:188408400-188409800	Genic enhancers	HSMMtube	muscle
41	chr2:188408400-188409800	Strong transcription	K562	blood
42	chr2:188408600-188410600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:188408600-188411600	Enhancers	NHLF	lung
44	chr2:188408600-188412600	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr2:188408600-188413200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:188408600-188413600	Enhancers	Hela-S3	cervix
47	chr2:188408600-188414600	Enhancers	NHDF-Ad	bronchial
48	chr2:188408800-188410600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:188408800-188411600	Genic enhancers	Muscle Satellite Cultured Cells	--
50	chr2:188409000-188410000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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