Variant report

Variant	rs41309108
Chromosome Location	chr2:231065722-231065723
allele	A/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	chr2:231065512-231066089	GM12892	blood:	n/a	n/a
2	POLR2A	chr2:231065483-231065989	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:231065624-231066013	GM12892	blood:	n/a	n/a
4	POLR2A	chr2:231065713-231065970	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:231065336..231067742-chr2:231072287..231074738,2	K562	blood:
2	chr2:231064688..231066515-chr2:231075264..231078231,2	K562	blood:
3	chr2:231064805..231066676-chr2:231078094..231080853,2	MCF-7	breast:

Variant related genes	Relation type
SP140	TF binding region
ENSG00000135899	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10168052	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10177277	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10755048	0.93[ASN][1000 genomes]
rs10755049	0.93[ASN][1000 genomes]
rs10755050	0.93[ASN][1000 genomes]
rs10804364	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10933328	0.93[ASN][1000 genomes]
rs1124534	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11556887	0.84[EUR][1000 genomes]
rs12474611	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12474616	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12474683	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12615975	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12616762	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12618921	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12619729	0.92[ASN][1000 genomes]
rs12619732	0.93[ASN][1000 genomes]
rs1469345	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1896258	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1896259	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1978583	0.93[ASN][1000 genomes]
rs1985603	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081714	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2114592	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396709	0.93[ASN][1000 genomes]
rs2396711	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3769837	0.96[ASN][1000 genomes]
rs3769839	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41345344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41423848	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4327229	0.93[ASN][1000 genomes]
rs4327230	0.90[ASN][1000 genomes]
rs4972942	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4973285	0.93[ASN][1000 genomes]
rs4973286	0.93[ASN][1000 genomes]
rs4973287	0.93[ASN][1000 genomes]
rs4973288	0.93[ASN][1000 genomes]
rs4973289	0.93[ASN][1000 genomes]
rs4973290	0.95[ASN][1000 genomes]
rs4973291	0.93[ASN][1000 genomes]
rs4973292	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4973293	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4973294	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4973296	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4973297	0.96[ASN][1000 genomes]
rs4973298	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs55809057	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55945652	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55956818	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56159955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56275915	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56301614	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56412815	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59536070	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61182521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6436919	0.83[ASN][1000 genomes]
rs6735604	0.83[ASN][1000 genomes]
rs6743028	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs67469122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750748	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6752361	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6755998	0.82[ASN][1000 genomes]
rs72982403	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982411	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982413	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72982416	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982421	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982424	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73000348	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73000367	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73000371	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561924	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7583769	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7592927	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7603350	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9061	0.86[EUR][1000 genomes]
rs930031	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs930032	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs958978	0.81[AFR][1000 genomes];0.92[ASN][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	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr2:231028400-231067000	Strong transcription	Primary B cells from peripheral blood	blood
2	chr2:231035400-231077000	Weak transcription	HepG2	liver
3	chr2:231036800-231071800	Weak transcription	NHEK	skin
4	chr2:231036800-231073600	Weak transcription	HMEC	breast
5	chr2:231038000-231069600	Weak transcription	NHLF	lung
6	chr2:231046200-231069800	Weak transcription	HSMM	muscle
7	chr2:231059000-231082800	Weak transcription	Stomach Mucosa	stomach
8	chr2:231061000-231067000	Weak transcription	Brain Angular Gyrus	brain
9	chr2:231062200-231081600	Strong transcription	Liver	Liver
10	chr2:231062400-231066800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:231062400-231074000	Strong transcription	Primary T cells from cord blood	blood
12	chr2:231062400-231081600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:231062600-231066000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:231062600-231066000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:231062600-231066000	Strong transcription	Colon Smooth Muscle	Colon
16	chr2:231062600-231066200	Strong transcription	Thymus	Thymus
17	chr2:231062600-231067600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr2:231062600-231069400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:231062600-231069600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:231062600-231073200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:231062600-231073600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:231062600-231079200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr2:231062600-231080600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:231062600-231081400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:231062600-231081400	Strong transcription	Adipose Nuclei	Adipose
26	chr2:231062600-231081400	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:231062600-231081400	Strong transcription	Fetal Thymus	thymus
28	chr2:231062600-231081600	Strong transcription	Fetal Lung	lung
29	chr2:231062600-231081600	Strong transcription	Placenta	Placenta
30	chr2:231062600-231081600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr2:231062600-231081600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:231062600-231081800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr2:231062600-231082200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:231062600-231082400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:231062600-231084200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr2:231062800-231066200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr2:231062800-231066200	Strong transcription	Left Ventricle	heart
38	chr2:231062800-231066400	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr2:231062800-231080600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr2:231062800-231081000	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:231063000-231067600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:231063000-231069600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:231063000-231071800	Weak transcription	NHDF-Ad	bronchial
44	chr2:231063000-231073400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:231063000-231077000	Weak transcription	Psoas Muscle	Psoas
46	chr2:231063000-231080200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:231063000-231084000	Weak transcription	Hela-S3	cervix
48	chr2:231063200-231066000	Strong transcription	Brain Hippocampus Middle	brain
49	chr2:231063200-231067000	Strong transcription	Primary B cells from cord blood	blood
50	chr2:231063200-231067000	Weak transcription	Placenta Amnion	Placenta Amnion

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