Variant report

Variant	rs60969946
Chromosome Location	chr2:183812267-183812268
allele	C/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	chr2:183810116-183812276	K562	blood:	n/a	n/a

Variant related genes	Relation type
NCKAP1	TF binding region

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10185562	0.90[AFR][1000 genomes]
rs10185998	0.81[AFR][1000 genomes]
rs1400128	0.84[AFR][1000 genomes]
rs16823916	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823924	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823929	0.91[EUR][1000 genomes]
rs2063873	0.90[AFR][1000 genomes]
rs2368350	0.84[AFR][1000 genomes]
rs2675114	0.85[ASN][1000 genomes]
rs2675115	0.83[ASN][1000 genomes]
rs3791247	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3817313	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57203160	0.83[EUR][1000 genomes]
rs72888404	1.00[ASN][1000 genomes]
rs908437	0.84[AFR][1000 genomes]
rs963107	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757842	chr2:183437700-183835084	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759104	chr2:183437700-183835084	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv818096	chr2:183701588-183827018	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv3693446	chr2:183785598-183833514	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183773400-183866000	Weak transcription	Colonic Mucosa	Colon
2	chr2:183773400-183877800	Weak transcription	Stomach Mucosa	stomach
3	chr2:183775600-183833000	Weak transcription	Pancreas	Pancrea
4	chr2:183780400-183874800	Weak transcription	Esophagus	oesophagus
5	chr2:183782200-183814200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:183785800-183824200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:183786400-183814200	Weak transcription	Aorta	Aorta
8	chr2:183786600-183826600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:183787000-183824000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:183788000-183830000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:183788200-183845600	Weak transcription	Lung	lung
12	chr2:183789200-183836400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:183789600-183812600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:183790200-183814400	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:183790800-183824200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:183793400-183840800	Weak transcription	Fetal Brain Male	brain
17	chr2:183793600-183814400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:183793600-183823800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:183793600-183826600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:183795200-183824200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:183795400-183814600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:183795400-183857600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:183798600-183814200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:183798600-183847000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:183800200-183817200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:183800400-183812600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:183802600-183814000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:183802800-183814400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:183802800-183817800	Weak transcription	Fetal Brain Female	brain
30	chr2:183803400-183815400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:183803800-183826600	Weak transcription	Brain Germinal Matrix	brain
32	chr2:183803800-183826600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:183804200-183813400	Weak transcription	HSMMtube	muscle
34	chr2:183804800-183859600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:183805600-183814400	Weak transcription	Placenta	Placenta
36	chr2:183805600-183874400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:183806000-183814800	Strong transcription	HSMM	muscle
38	chr2:183806400-183813400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:183806800-183813600	Weak transcription	HMEC	breast
40	chr2:183807400-183813400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:183807400-183824200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:183808200-183812600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:183809200-183812400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr2:183810200-183812600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:183810200-183814200	Weak transcription	Fetal Intestine Small	intestine
46	chr2:183810400-183812400	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr2:183810800-183813200	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:183811200-183812400	Strong transcription	HepG2	liver
49	chr2:183811200-183812400	Genic enhancers	Osteobl	bone
50	chr2:183811600-183812400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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