Variant report

Variant	rs12712656
Chromosome Location	chr2:39993952-39993953
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:39993900-39994050	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39662097..39664715-chr2:39993095..39995663,2	K562	blood:

Variant related genes	Relation type
THUMPD2	TF binding region
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10164984	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10169390	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10174709	0.86[EUR][1000 genomes]
rs10206408	0.87[EUR][1000 genomes]
rs10207589	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10211306	0.84[EUR][1000 genomes]
rs1035138	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1035139	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11124691	0.87[EUR][1000 genomes]
rs11124692	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11124693	0.88[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11684302	0.81[CEU][hapmap]
rs12470473	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs12617624	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12620957	0.88[EUR][1000 genomes]
rs12623462	0.83[EUR][1000 genomes]
rs12623545	0.87[EUR][1000 genomes]
rs12624217	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13026313	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs13400213	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425906	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13428837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1548877	0.86[EUR][1000 genomes]
rs17478972	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861243	0.84[ASN][1000 genomes]
rs1861258	0.82[CEU][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1986876	1.00[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2041735	0.82[EUR][1000 genomes]
rs2192685	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241115	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs2373689	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2540228	0.80[EUR][1000 genomes]
rs2716730	0.80[CEU][hapmap]
rs35761077	0.91[EUR][1000 genomes]
rs3732121	0.81[EUR][1000 genomes]
rs3732122	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs3815510	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs4670955	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4670956	0.80[CEU][hapmap]
rs4670957	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs4670958	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs4670959	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59756273	0.83[EUR][1000 genomes]
rs6544242	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs6719179	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6722610	0.83[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs727376	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7560642	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7581406	0.87[EUR][1000 genomes]
rs7590912	0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8265	0.84[CEU][hapmap];0.90[CHB][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs917960	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs917961	0.90[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs917963	0.88[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs9309042	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs962262	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs997976	0.92[CEU][hapmap];0.83[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	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:39971000-39999800	Weak transcription	Right Ventricle	heart
5	chr2:39971600-39998800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:39972400-39998600	Strong transcription	HMEC	breast
7	chr2:39972400-39998800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:39973000-39998800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:39974200-39998600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:39974600-39994000	Strong transcription	Fetal Thymus	thymus
11	chr2:39975000-39998400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:39975000-39999800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:39975400-39997000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:39975800-39994600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:39976200-39995400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:39976200-39998800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:39976800-39999000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:39978600-40000000	Weak transcription	Fetal Heart	heart
19	chr2:39983000-39999200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:39983200-39994000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:39983600-39994200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:39983600-39996400	Strong transcription	NHDF-Ad	bronchial
23	chr2:39983600-39998600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:39983600-39999000	Strong transcription	HSMM	muscle
25	chr2:39984800-39999600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:39985000-39995400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:39985000-39996000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:39985000-40005000	Weak transcription	Colonic Mucosa	Colon
29	chr2:39985200-39996000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:39985200-39998400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:39985200-39999600	Weak transcription	Brain Germinal Matrix	brain
32	chr2:39985200-39999600	Weak transcription	Psoas Muscle	Psoas
33	chr2:39985200-39999800	Weak transcription	Brain Substantia Nigra	brain
34	chr2:39985200-40005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:39985400-40005200	Weak transcription	Fetal Brain Male	brain
36	chr2:39985600-40001000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr2:39985800-39995600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:39985800-39995800	Weak transcription	Stomach Mucosa	stomach
39	chr2:39985800-39996000	Weak transcription	Esophagus	oesophagus
40	chr2:39985800-39996000	Weak transcription	Gastric	stomach
41	chr2:39985800-39996000	Weak transcription	Pancreas	Pancrea
42	chr2:39985800-39996200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:39985800-39996200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:39985800-39996400	Weak transcription	Fetal Intestine Small	intestine
45	chr2:39985800-39999200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:39985800-39999400	Weak transcription	Aorta	Aorta
47	chr2:39985800-39999600	Weak transcription	Brain Angular Gyrus	brain
48	chr2:39985800-39999800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:39985800-39999800	Weak transcription	Small Intestine	intestine
50	chr2:39985800-40004800	Weak transcription	Fetal Brain Female	brain

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