Variant report

Variant	rs28370108
Chromosome Location	chr1:223946089-223946090
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	chr1:223945770-223946457	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr1:223945792-223946370	K562	blood:	n/a	n/a
3	POLR2A	chr1:223945848-223946292	HCT-116	colon:	n/a	n/a
4	POLR2A	chr1:223945873-223946420	A549	lung:	n/a	n/a
5	POLR2A	chr1:223946060-223946180	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:223937857-223950461	K562	blood:	n/a	n/a
7	POLR2A	chr1:223945943-223948408	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:223946052-223946327	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:223946051-223946156	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CAPN2	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10753427	1.00[AMR][1000 genomes]
rs10799364	1.00[AMR][1000 genomes]
rs10915854	1.00[AMR][1000 genomes]
rs10916015	1.00[AMR][1000 genomes]
rs1222144	1.00[AMR][1000 genomes]
rs1361915	1.00[AMR][1000 genomes]
rs1539703	1.00[AMR][1000 genomes]
rs16842210	1.00[AMR][1000 genomes]
rs16842251	1.00[AMR][1000 genomes]
rs1857549	1.00[AMR][1000 genomes]
rs1892071	1.00[AMR][1000 genomes]
rs1892074	1.00[AMR][1000 genomes]
rs1892075	1.00[AMR][1000 genomes]
rs1977898	1.00[AMR][1000 genomes]
rs2000317	1.00[AMR][1000 genomes]
rs2096343	1.00[AMR][1000 genomes]
rs2154115	1.00[AMR][1000 genomes]
rs2186005	1.00[AMR][1000 genomes]
rs2404288	1.00[AMR][1000 genomes]
rs25655	1.00[AMR][1000 genomes]
rs28370086	1.00[AMR][1000 genomes]
rs28370105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4653792	1.00[AMR][1000 genomes]
rs4653866	1.00[AMR][1000 genomes]
rs4653869	1.00[AMR][1000 genomes]
rs6422641	1.00[AMR][1000 genomes]
rs6688648	1.00[AMR][1000 genomes]
rs7538151	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7554290	1.00[AMR][1000 genomes]
rs9660081	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv520609	chr1:223931411-223947081	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv521758	chr1:223931411-223954080	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223931200-223954800	Strong transcription	HMEC	breast
2	chr1:223931400-223954400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:223935800-223952600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:223936600-223954800	Strong transcription	NHEK	skin
5	chr1:223936800-223947400	Weak transcription	Fetal Brain Male	brain
6	chr1:223936800-223954400	Strong transcription	HSMM	muscle
7	chr1:223937000-223947600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:223937000-223948000	Strong transcription	Lung	lung
9	chr1:223937000-223948200	Weak transcription	Right Atrium	heart
10	chr1:223937000-223951200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:223937000-223954400	Strong transcription	Colonic Mucosa	Colon
12	chr1:223937000-223954400	Strong transcription	Esophagus	oesophagus
13	chr1:223937000-223954400	Strong transcription	Gastric	stomach
14	chr1:223937000-223954800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:223937000-223954800	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:223937000-223954800	Strong transcription	NHDF-Ad	bronchial
19	chr1:223937000-223954800	Strong transcription	Osteobl	bone
20	chr1:223937000-223957200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
23	chr1:223937200-223948600	Strong transcription	HUVEC	blood vessel
24	chr1:223937200-223951800	Strong transcription	HSMMtube	muscle
25	chr1:223937200-223952600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:223937200-223953000	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:223937200-223954800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:223937200-223954800	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:223937200-223954800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:223937200-223954800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
33	chr1:223937400-223948600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:223937400-223948600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:223937400-223951000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:223937400-223952600	Strong transcription	NH-A	brain
37	chr1:223937400-223952800	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:223937400-223952800	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:223937400-223953000	Strong transcription	Adipose Nuclei	Adipose
40	chr1:223937400-223954400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr1:223937400-223954400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:223937400-223954400	Strong transcription	NHLF	lung
43	chr1:223937400-223954800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:223937400-223954800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:223937400-223954800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:223937400-223954800	Strong transcription	Fetal Stomach	stomach
47	chr1:223937400-223954800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr1:223937400-223954800	Strong transcription	A549	lung
49	chr1:223937600-223954200	Strong transcription	Left Ventricle	heart
50	chr1:223937600-223954800	Strong transcription	Stomach Smooth Muscle	stomach

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