Variant report

Variant	rs28999676
Chromosome Location	chr8:103248800-103248801
allele	A/G
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	CHD1	chr8:103248792-103252333	IMR90	lung:	n/a	chr8:103251203-103251213
2	STAT3	chr8:103248790-103249907	MCF10A-Er-Src	breast:	n/a	chr8:103249108-103249119
3	POLR2A	chr8:103248763-103252162	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr8:103248635-103249587	GM12878	blood:	n/a	n/a
5	POLR2A	chr8:103248497-103249913	GM12878	blood:	n/a	n/a
6	CHD1	chr8:103248610-103251204	GM12878	blood:	n/a	n/a
7	POLR2A	chr8:103248725-103251275	GM12891	blood:	n/a	n/a
8	STAT3	chr8:103248643-103249469	MCF10A-Er-Src	breast:	n/a	chr8:103249108-103249119

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:103248705..103250283-chr8:103601762..103604480,2	K562	blood:
2	chr8:103248364..103250740-chr8:103821721..103824052,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246263	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10505019	0.80[ASN][1000 genomes]
rs1052069	0.80[ASN][1000 genomes]
rs1052071	0.80[ASN][1000 genomes]
rs11774420	0.93[ASN][1000 genomes]
rs11774459	0.93[ASN][1000 genomes]
rs11776865	0.80[ASN][1000 genomes]
rs11777942	0.93[ASN][1000 genomes]
rs11778107	0.93[ASN][1000 genomes]
rs11783467	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784180	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11784534	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11785514	0.80[ASN][1000 genomes]
rs11786397	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16869269	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16869276	0.93[ASN][1000 genomes]
rs16869282	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869295	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs16918482	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2387995	0.93[ASN][1000 genomes]
rs28928571	0.93[ASN][1000 genomes]
rs28928592	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28928597	0.93[ASN][1000 genomes]
rs28999671	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28999706	0.93[ASN][1000 genomes]
rs29000274	0.93[ASN][1000 genomes]
rs29000286	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs29000294	0.80[ASN][1000 genomes]
rs3735720	0.80[ASN][1000 genomes]
rs3735721	0.80[ASN][1000 genomes]
rs3735722	0.93[ASN][1000 genomes]
rs3907099	0.80[ASN][1000 genomes]
rs4329248	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5005121	0.80[ASN][1000 genomes]
rs57901015	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57978361	0.81[AMR][1000 genomes]
rs60604862	0.80[ASN][1000 genomes]
rs7836046	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7841131	0.80[AFR][1000 genomes];0.93[ASN][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	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv891242	chr8:103210971-103282418	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv891243	chr8:103219629-103292724	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:155 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103220400-103248800	Weak transcription	Hela-S3	cervix
2	chr8:103231600-103249800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:103234600-103250000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr8:103238200-103248800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr8:103238400-103248800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:103240800-103248800	Weak transcription	Pancreas	Pancrea
7	chr8:103240800-103249000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr8:103240800-103249000	Weak transcription	Gastric	stomach
9	chr8:103241000-103248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:103241000-103248800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr8:103241000-103249000	Weak transcription	Right Ventricle	heart
12	chr8:103241000-103249200	Weak transcription	Colonic Mucosa	Colon
13	chr8:103241000-103250400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:103241000-103250400	Weak transcription	Esophagus	oesophagus
15	chr8:103241200-103249000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr8:103241200-103249000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr8:103241400-103249600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr8:103241400-103250600	Weak transcription	Spleen	Spleen
19	chr8:103242000-103249400	Weak transcription	Fetal Stomach	stomach
20	chr8:103242600-103249200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr8:103243400-103249800	Weak transcription	Fetal Kidney	kidney
22	chr8:103243600-103248800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr8:103243600-103249200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr8:103243600-103250200	Weak transcription	Placenta	Placenta
25	chr8:103243800-103248800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr8:103243800-103249000	Weak transcription	Fetal Thymus	thymus
27	chr8:103243800-103249200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr8:103243800-103249800	Weak transcription	Brain Germinal Matrix	brain
29	chr8:103244000-103249800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr8:103244400-103248800	Weak transcription	Liver	Liver
31	chr8:103244400-103248800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr8:103244400-103249000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr8:103244400-103250400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr8:103244600-103248800	Weak transcription	Fetal Lung	lung
35	chr8:103244800-103248800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr8:103245600-103249000	Weak transcription	Right Atrium	heart
37	chr8:103246000-103249000	Weak transcription	Fetal Intestine Large	intestine
38	chr8:103246200-103249000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr8:103246600-103248800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr8:103246800-103248800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr8:103246800-103249200	Weak transcription	Fetal Intestine Small	intestine
42	chr8:103247400-103248800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr8:103247600-103249200	Enhancers	Fetal Brain Male	brain
44	chr8:103248000-103249000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr8:103248000-103249200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr8:103248000-103249200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr8:103248000-103249200	Enhancers	Left Ventricle	heart
48	chr8:103248000-103249400	Enhancers	Colon Smooth Muscle	Colon
49	chr8:103248000-103249600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr8:103248000-103250000	Enhancers	Skeletal Muscle Male	skeletal muscle

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