Variant report

Variant	rs3731748
Chromosome Location	chr2:179413110-179413111
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	chr2:179410631-179414899	K562	blood:	n/a	n/a
2	POLR2A	chr2:179412963-179413699	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:179411316..179413406-chr2:179423053..179424886,2	K562	blood:
2	chr2:179395497..179400266-chr2:179412543..179417721,4	K562	blood:
3	chr2:179410068..179413369-chr2:179416784..179418965,3	K562	blood:

Variant related genes	Relation type
ENSG00000270277	TF binding region
ENSG00000237298	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1007025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614435	0.91[CEU][hapmap];0.86[GIH][hapmap]
rs12618265	1.00[CEU][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12998857	0.91[CEU][hapmap]
rs13005601	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13009158	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13029629	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13034990	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16866358	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16866365	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16866369	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16866373	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16866397	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16866406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2288325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288569	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2288571	0.91[CEU][hapmap]
rs2303539	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303828	0.86[GIH][hapmap]
rs2303838	0.82[GIH][hapmap]
rs2857265	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3731746	0.83[CEU][hapmap];0.84[GIH][hapmap]
rs3731749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731751	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829747	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829748	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6755456	0.91[CEU][hapmap]
rs744426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7597154	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs890578	0.91[CEU][hapmap];0.84[GIH][hapmap]

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	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv2757841	chr2:179409072-179608242	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2759103	chr2:179409072-179608242	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179417600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:179388800-179429400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:179388800-179441800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:179388800-179448800	Weak transcription	Small Intestine	intestine
5	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:179389400-179413400	Weak transcription	NH-A	brain
7	chr2:179389400-179416800	Weak transcription	Stomach Mucosa	stomach
8	chr2:179389400-179417200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:179389400-179417200	Weak transcription	NHDF-Ad	bronchial
10	chr2:179389400-179417200	Weak transcription	NHLF	lung
11	chr2:179389400-179428200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:179390600-179426400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:179391200-179419200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:179393800-179439800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:179394800-179413400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:179394800-179417600	Strong transcription	HSMMtube	muscle
17	chr2:179394800-179421600	Strong transcription	Left Ventricle	heart
18	chr2:179395400-179414200	Strong transcription	Fetal Thymus	thymus
19	chr2:179395400-179423000	Strong transcription	Fetal Muscle Trunk	muscle
20	chr2:179395600-179414200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:179395600-179421600	Strong transcription	Fetal Heart	heart
22	chr2:179395800-179414000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:179395800-179414200	Strong transcription	Dnd41	blood
24	chr2:179396000-179413800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:179396000-179414600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:179396000-179415800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr2:179396000-179417600	Strong transcription	HSMM	muscle
28	chr2:179396000-179422400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:179396000-179445400	Strong transcription	Right Ventricle	heart
30	chr2:179396200-179414200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:179396200-179414800	Strong transcription	Pancreas	Pancrea
32	chr2:179396200-179419800	Strong transcription	Fetal Intestine Large	intestine
33	chr2:179396200-179420200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:179396400-179419800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:179396400-179420000	Strong transcription	Primary B cells from cord blood	blood
36	chr2:179396600-179432400	Weak transcription	Fetal Kidney	kidney
37	chr2:179397200-179417600	Weak transcription	A549	lung
38	chr2:179397800-179417600	Weak transcription	NHEK	skin
39	chr2:179398200-179417600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:179399200-179418800	Weak transcription	Fetal Brain Female	brain
41	chr2:179400000-179414600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:179400600-179414000	Strong transcription	Spleen	Spleen
43	chr2:179401600-179414200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:179403400-179414200	Strong transcription	Thymus	Thymus
45	chr2:179403600-179419800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:179404600-179418000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:179404800-179417200	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:179405000-179413200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:179405000-179417400	Weak transcription	Osteobl	bone
50	chr2:179405200-179427000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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