Variant report

Variant	rs11125979
Chromosome Location	chr2:63824306-63824307
allele	G/T
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	POLR2A	chr2:63820532-63825081	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63814544..63817562-chr2:63819288..63824360,10	K562	blood:
2	chr2:63814652..63820726-chr2:63822860..63830564,18	K562	blood:

Variant related genes	Relation type
MDH1	TF binding region
ENSG00000143951	Chromatin interaction
ENSG00000014641	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10164844	0.82[JPT][hapmap]
rs10171190	0.80[CHB][hapmap]
rs10200146	0.81[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs10209490	0.80[CHB][hapmap]
rs1022351	0.80[CHB][hapmap]
rs1022353	0.80[CHB][hapmap]
rs11676682	0.90[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11694892	0.94[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap]
rs12104978	0.85[ASN][1000 genomes]
rs12995715	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13409031	0.80[CHB][hapmap]
rs13422170	0.80[CHB][hapmap]
rs169035	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1869700	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1878505	0.90[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs2028886	0.90[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes]
rs2034270	0.88[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs2138791	0.80[CHB][hapmap]
rs2178678	0.80[CHB][hapmap]
rs2421892	0.80[CHB][hapmap]
rs2421954	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2422008	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs2592389	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs262496	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs262497	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs262498	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs262499	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs262500	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35516797	0.84[EUR][1000 genomes]
rs3754540	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671061	0.80[CHB][hapmap]
rs4671511	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6731136	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs6731877	0.83[ASN][1000 genomes]
rs6735907	0.85[CHB][hapmap]
rs6737621	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6756850	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7598973	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs8179835	0.90[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv1792289	chr2:63812148-63900292	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats 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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63816600-63830200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:63816800-63831000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:63817000-63827000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:63817000-63827000	Weak transcription	Spleen	Spleen
5	chr2:63817000-63827400	Weak transcription	Lung	lung
6	chr2:63817000-63828800	Weak transcription	Pancreas	Pancrea
7	chr2:63817000-63830200	Weak transcription	Esophagus	oesophagus
8	chr2:63817000-63831800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:63817200-63828000	Weak transcription	Aorta	Aorta
10	chr2:63817200-63834400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:63817400-63831600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:63817600-63828600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:63818000-63834800	Strong transcription	Fetal Thymus	thymus
14	chr2:63818000-63835400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:63818400-63828000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:63818400-63829800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:63818400-63831000	Weak transcription	Gastric	stomach
18	chr2:63818400-63831800	Weak transcription	Colonic Mucosa	Colon
19	chr2:63818400-63831800	Weak transcription	Small Intestine	intestine
20	chr2:63818600-63834800	Strong transcription	Primary T cells from cord blood	blood
21	chr2:63818600-63835800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:63818800-63831800	Weak transcription	Fetal Brain Male	brain
23	chr2:63818800-63832000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:63819000-63827400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:63819200-63825800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:63819200-63835000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:63819400-63827200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:63819400-63829200	Strong transcription	Fetal Muscle Leg	muscle
29	chr2:63819400-63834800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:63819600-63834800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:63819800-63829400	Strong transcription	Left Ventricle	heart
32	chr2:63820200-63834800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:63820200-63834800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:63820200-63835200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:63820400-63825000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:63820400-63828600	Strong transcription	Fetal Lung	lung
37	chr2:63820400-63829600	Strong transcription	HMEC	breast
38	chr2:63820400-63834600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:63820400-63834800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:63820400-63835000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:63820400-63835000	Strong transcription	Liver	Liver
42	chr2:63820600-63824800	Strong transcription	Primary B cells from cord blood	blood
43	chr2:63820600-63824800	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr2:63820600-63825000	Genic enhancers	Adipose Nuclei	Adipose
45	chr2:63820600-63825200	Strong transcription	K562	blood
46	chr2:63820600-63826000	Strong transcription	NH-A	brain
47	chr2:63820600-63834200	Strong transcription	A549	lung
48	chr2:63820600-63834800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:63820600-63834800	Strong transcription	Placenta	Placenta
50	chr2:63820600-63835000	Strong transcription	Primary T cells fromperipheralblood	blood

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