Variant report

Variant	rs2246268
Chromosome Location	chr10:5800811-5800812
allele	A/C
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	chr10:5800276-5801187	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr10:5800210-5803709	MCF-7	breast:	n/a	n/a
3	POLR2A	chr10:5798429-5801163	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:5798629-5810250	K562	blood:	n/a	n/a
5	POLR2A	chr10:5798571-5803731	GM12891	blood:	n/a	n/a
6	POLR2A	chr10:5800460-5804303	GM12878	blood:	n/a	n/a
7	POLR2A	chr10:5800686-5801228	HepG2	liver:	n/a	n/a
8	POLR2A	chr10:5800330-5800854	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr10:5800507-5800827	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr10:5799552-5801076	HepG2	liver:	n/a	n/a
11	POLR2A	chr10:5800381-5800832	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5488455..5489986-chr10:5798808..5801321,2	MCF-7	breast:
2	chr10:5659054..5661643-chr10:5799141..5801779,2	MCF-7	breast:

Variant related genes	Relation type
FAM208B	TF binding region
ENSG00000173848	Chromatin interaction
ENSG00000228951	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11254115	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11254828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11254898	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11255139	0.82[ASN][1000 genomes]
rs12257412	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12571055	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12572339	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1567708	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2275772	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2669133	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2669139	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2797490	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2797492	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2797497	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34404996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3750636	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3793708	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3793714	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs3924378	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs57103262	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58502403	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59827083	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7089693	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7096328	0.88[ASN][1000 genomes]
rs73610559	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7893673	0.82[AMR][1000 genomes]
rs7908235	0.91[JPT][hapmap]

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	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5762600-5843400	Strong transcription	Dnd41	blood
2	chr10:5762800-5843000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:5768000-5849400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:5779000-5804600	Strong transcription	A549	lung
5	chr10:5781400-5818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr10:5783400-5816600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr10:5784800-5818000	Weak transcription	Stomach Mucosa	stomach
8	chr10:5786200-5816400	Weak transcription	Right Atrium	heart
9	chr10:5788000-5818000	Strong transcription	Duodenum Mucosa	Duodenum
10	chr10:5789200-5804400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr10:5794000-5802600	Strong transcription	Fetal Stomach	stomach
12	chr10:5794600-5806600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr10:5795000-5817800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr10:5795200-5804200	Strong transcription	Fetal Intestine Small	intestine
15	chr10:5796000-5822400	Strong transcription	Fetal Intestine Large	intestine
16	chr10:5797200-5804200	Strong transcription	Thymus	Thymus
17	chr10:5797200-5819000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr10:5797400-5816600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr10:5797400-5816800	Strong transcription	Fetal Thymus	thymus
20	chr10:5797400-5847400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr10:5797600-5803600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:5797600-5804200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr10:5797600-5805600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr10:5797600-5807800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr10:5797600-5811800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
26	chr10:5797600-5812200	Strong transcription	Primary hematopoietic stem cells	blood
27	chr10:5797600-5812200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr10:5797600-5812400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr10:5797600-5814600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr10:5797600-5816200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:5797600-5817200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr10:5797600-5817800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr10:5797600-5817800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr10:5797800-5811200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr10:5797800-5812000	Strong transcription	Primary T cells from cord blood	blood
36	chr10:5797800-5816400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr10:5798000-5803200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr10:5798000-5803600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr10:5798000-5803800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr10:5798000-5804200	Strong transcription	Brain Anterior Caudate	brain
41	chr10:5798000-5812600	Strong transcription	HMEC	breast
42	chr10:5798000-5817000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:5798000-5817600	Strong transcription	Primary B cells from cord blood	blood
44	chr10:5798000-5818200	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr10:5798000-5842800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr10:5798200-5815400	Strong transcription	NH-A	brain
47	chr10:5798200-5817000	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr10:5798200-5843000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr10:5798400-5801800	Strong transcription	Colonic Mucosa	Colon
50	chr10:5798400-5803200	Strong transcription	Psoas Muscle	Psoas

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