Variant report

Variant	rs11163925
Chromosome Location	chr1:84705494-84705495
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	chr1:84704853-84705760	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84703877..84705548-chr1:84707085..84709584,2	K562	blood:

Variant related genes	Relation type
ENSG00000226970	TF binding region

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10782825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12070215	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12126586	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12134263	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12135635	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12142220	0.82[CEU][hapmap]
rs17131308	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17131371	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2811994	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs585992	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs600771	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs601301	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs605969	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs606816	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs606904	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs608672	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61766401	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs620856	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs621670	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs621750	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs643521	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs663630	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9943254	0.88[AMR][1000 genomes];0.87[EUR][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	nsv871538	chr1:84633116-84717983	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv1816427	chr1:84670816-84715634	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv1823244	chr1:84670816-84715634	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv1824568	chr1:84670816-84715634	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv1822734	chr1:84678418-84715634	ZNF genes & repeats Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	esv1845114	chr1:84678418-84715634	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	esv1851921	chr1:84678418-84715634	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	esv1824421	chr1:84704329-84719245	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84657600-84708000	Weak transcription	Left Ventricle	heart
2	chr1:84666800-84710200	Weak transcription	HSMMtube	muscle
3	chr1:84672600-84711200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:84675200-84712800	Weak transcription	NH-A	brain
5	chr1:84685400-84705600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:84685600-84713400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:84690000-84719400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:84690200-84707400	Weak transcription	Right Ventricle	heart
9	chr1:84690400-84711800	Weak transcription	Spleen	Spleen
10	chr1:84691200-84712200	Weak transcription	Pancreas	Pancrea
11	chr1:84691400-84707000	Weak transcription	Fetal Stomach	stomach
12	chr1:84699000-84707000	Weak transcription	Psoas Muscle	Psoas
13	chr1:84699600-84713000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:84699800-84711600	Weak transcription	A549	lung
15	chr1:84700400-84706200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:84700600-84705800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr1:84700600-84705800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:84700600-84705800	Strong transcription	Brain Hippocampus Middle	brain
19	chr1:84700600-84706000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr1:84700600-84706200	Strong transcription	Fetal Thymus	thymus
21	chr1:84700600-84706200	Strong transcription	Dnd41	blood
22	chr1:84700600-84706600	Strong transcription	Primary T cells from cord blood	blood
23	chr1:84700600-84706600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:84700800-84705600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:84700800-84706200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:84701200-84705600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:84701200-84706000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:84701200-84707000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:84701200-84707000	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:84701200-84707200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:84701200-84707600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:84701200-84711800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:84701200-84713200	Weak transcription	Colonic Mucosa	Colon
34	chr1:84701200-84717400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:84701200-84718400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:84701200-84719600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:84701400-84705800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:84701400-84705800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:84701400-84706000	Strong transcription	Primary B cells from cord blood	blood
40	chr1:84701400-84706800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:84701400-84707200	Weak transcription	Liver	Liver
42	chr1:84701400-84707200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:84701400-84707600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:84701400-84707600	Weak transcription	Fetal Brain Male	brain
45	chr1:84701400-84707600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:84701400-84708000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:84701400-84713000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:84701400-84713000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:84701400-84719800	Weak transcription	Fetal Heart	heart
50	chr1:84701400-84719800	Weak transcription	HSMM	muscle

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