Variant report

Variant	rs2928616
Chromosome Location	chr8:6562698-6562699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:6559932-6562803	GM18505	blood:	n/a	n/a
2	POLR2A	chr8:6562403-6562961	GM12892	blood:	n/a	n/a
3	POLR2A	chr8:6559448-6562834	GM12878	blood:	n/a	n/a
4	MTA3	chr8:6559306-6562905	GM12878	blood:	n/a	n/a
5	NFATC1	chr8:6559472-6563219	GM12878	blood:	n/a	n/a
6	WRNIP1	chr8:6562608-6562774	GM12878	blood:	n/a	n/a
7	POLR2A	chr8:6561882-6562885	GM12892	blood:	n/a	n/a
8	POLR2A	chr8:6557803-6562956	GM12891	blood:	n/a	n/a
9	POLR2A	chr8:6561887-6562802	GM12878	blood:	n/a	n/a
10	POLR2A	chr8:6562080-6562901	GM12878	blood:	n/a	n/a
11	POLR2A	chr8:6560939-6562896	GM12892	blood:	n/a	n/a
12	POLR2A	chr8:6559898-6568153	GM12892	blood:	n/a	n/a
13	NFATC1	chr8:6560662-6562743	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:6558068..6559956-chr8:6562512..6564020,2	K562	blood:
2	chr8:6559614..6563740-chr8:6564058..6567260,6	K562	blood:
3	chr8:6560106..6562709-chr8:6563972..6565977,4	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANGPT2-10	chr8:6562294-6562900	NONHSAT124783
2	lnc-ANGPT2-10	chr8:6560412-6563627	NONHSAT124784

No data

Variant related genes	Relation type
AGPAT5	TF binding region
ENSG00000155189	Chromatin interaction
ENSG00000249898	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10108451	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs11137064	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11986408	0.88[AFR][1000 genomes]
rs11986409	0.90[AFR][1000 genomes]
rs11996255	0.90[AFR][1000 genomes]
rs11996256	0.90[AFR][1000 genomes]
rs1425784	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1425785	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1425786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542849	1.00[CEU][hapmap]
rs1559745	1.00[CEU][hapmap]
rs1559747	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17077966	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17078011	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17078066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1834450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978547	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059537	0.98[ASN][1000 genomes]
rs2114060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272772	0.81[ASN][1000 genomes]
rs2277135	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28478952	0.83[ASN][1000 genomes]
rs2911981	1.00[CEU][hapmap]
rs2911986	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2911988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911989	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2911990	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2912073	1.00[CEU][hapmap]
rs2912083	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2928583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2928612	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2928614	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928615	0.82[EUR][1000 genomes]
rs2928622	1.00[CEU][hapmap]
rs2978949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2980687	1.00[CEU][hapmap]
rs2980691	1.00[CEU][hapmap]
rs3811118	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3811120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4840574	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4841551	0.98[ASN][1000 genomes]
rs4841594	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4841654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4841729	0.81[ASN][1000 genomes]
rs58725842	0.81[ASN][1000 genomes]
rs61622585	0.81[ASN][1000 genomes]
rs6988650	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6989392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6996843	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6996864	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6997196	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7003121	0.93[ASN][1000 genomes]
rs7008408	1.00[CHB][hapmap]
rs7016859	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs714508	1.00[CEU][hapmap]
rs7813375	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7825937	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7830784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7845315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9773764	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1021684	chr8:6350091-6809455	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv2422383	chr8:6362389-6781593	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS 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	23 gene(s)	inside rSNPs	diseases
7	nsv610004	chr8:6402366-6772913	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1029241	chr8:6411300-6761720	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv933075	chr8:6456475-7366650	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
10	nsv1025976	chr8:6472948-6686972	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv933768	chr8:6482944-6618221	Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv831220	chr8:6527845-6728491	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv1030637	chr8:6545498-6669949	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv1034115	chr8:6546984-6665832	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS 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 miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6543200-6565200	Weak transcription	Left Ventricle	heart
2	chr8:6543400-6564000	Weak transcription	Spleen	Spleen
3	chr8:6543600-6564200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:6548400-6563400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr8:6548400-6563600	Weak transcription	Thymus	Thymus
6	chr8:6548600-6563800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr8:6548600-6564400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr8:6548800-6564200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr8:6549400-6564000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr8:6549400-6565000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr8:6549600-6563600	Weak transcription	Primary T cells from cord blood	blood
12	chr8:6552000-6563600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr8:6552000-6565200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr8:6552000-6565200	Weak transcription	Pancreas	Pancrea
15	chr8:6552200-6563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr8:6552200-6564000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr8:6552400-6563600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr8:6552600-6563400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr8:6553000-6563800	Weak transcription	Gastric	stomach
20	chr8:6553400-6564200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr8:6554200-6563800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr8:6554200-6565200	Weak transcription	Aorta	Aorta
23	chr8:6554600-6565000	Weak transcription	Brain Hippocampus Middle	brain
24	chr8:6554800-6564600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr8:6555200-6563600	Weak transcription	Fetal Intestine Large	intestine
26	chr8:6555600-6564400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr8:6555600-6565200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr8:6555800-6563600	Weak transcription	Fetal Intestine Small	intestine
29	chr8:6556200-6563200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr8:6556200-6563600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr8:6556200-6564200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr8:6556800-6564000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr8:6556800-6564000	Weak transcription	Fetal Muscle Leg	muscle
34	chr8:6557000-6563800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr8:6557000-6565200	Weak transcription	Lung	lung
36	chr8:6557400-6563600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr8:6557400-6563800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr8:6557400-6563800	Weak transcription	Placenta	Placenta
39	chr8:6557400-6564200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr8:6557400-6565000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr8:6558000-6565000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr8:6558200-6563600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr8:6558200-6563800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr8:6558200-6564000	Weak transcription	HUVEC	blood vessel
45	chr8:6558200-6564600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr8:6558400-6563600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr8:6558600-6563600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr8:6558600-6563800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr8:6559000-6563600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr8:6559000-6564000	Weak transcription	Rectal Smooth Muscle	rectum

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