Variant report

Variant	rs11996256
Chromosome Location	chr8:6561017-6561018
allele	C/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	chr8:6559932-6562803	GM18505	blood:	n/a	n/a
2	E2F6	chr8:6560607-6561103	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr8:6560747-6561038	H1-hESC	embryonic stem cell:	n/a	chr8:6560883-6560893 chr8:6560909-6560919
4	POLR2A	chr8:6559448-6562834	GM12878	blood:	n/a	n/a
5	MTA3	chr8:6559306-6562905	GM12878	blood:	n/a	n/a
6	USF2	chr8:6560895-6561072	H1-hESC	embryonic stem cell:	n/a	n/a
7	NFATC1	chr8:6559472-6563219	GM12878	blood:	n/a	n/a
8	MAX	chr8:6560676-6561114	H1-hESC	embryonic stem cell:	n/a	chr8:6560883-6560893 chr8:6560909-6560919
9	POLR2A	chr8:6557803-6562956	GM12891	blood:	n/a	n/a
10	MTA3	chr8:6559724-6561414	GM12878	blood:	n/a	n/a
11	CTCF	chr8:6560648-6561047	MCF-7	breast:	n/a	n/a
12	BCLAF1	chr8:6560628-6561527	GM12878	blood:	n/a	n/a
13	POLR2A	chr8:6559559-6561781	GM12878	blood:	n/a	n/a
14	POLR2A	chr8:6560939-6562896	GM12892	blood:	n/a	n/a
15	POLR2A	chr8:6560794-6561877	GM12892	blood:	n/a	n/a
16	POLR2A	chr8:6559463-6561756	K562	blood:	n/a	n/a
17	STAT5A	chr8:6560402-6561762	GM12878	blood:	n/a	n/a
18	ZNF143	chr8:6560691-6561021	GM12878	blood:	n/a	n/a
19	ATF2	chr8:6559811-6561071	GM12878	blood:	n/a	n/a
20	ZNF384	chr8:6560881-6561164	GM12878	blood:	n/a	n/a
21	MAX	chr8:6560761-6561069	H1-hESC	embryonic stem cell:	n/a	chr8:6560883-6560893 chr8:6560909-6560919
22	CTCF	chr8:6560900-6561050	GM06990	blood:	n/a	n/a
23	MYC	chr8:6560740-6561042	K562	blood:	n/a	chr8:6560883-6560893 chr8:6560909-6560919
24	POLR2A	chr8:6561002-6561508	GM12891	blood:	n/a	n/a
25	POLR2A	chr8:6559898-6568153	GM12892	blood:	n/a	n/a
26	NFATC1	chr8:6560662-6562743	GM12878	blood:	n/a	n/a

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

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

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10108451	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11986408	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11986409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11996255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1365041	0.83[EUR][1000 genomes]
rs1559744	0.82[ASN][1000 genomes]
rs1978547	0.84[AFR][1000 genomes]
rs2059536	0.81[EUR][1000 genomes]
rs2114060	0.89[AFR][1000 genomes]
rs2162152	0.89[AFR][1000 genomes]
rs2408444	0.88[ASN][1000 genomes]
rs28476773	0.87[ASN][1000 genomes]
rs2911983	0.89[ASN][1000 genomes]
rs2911987	0.82[EUR][1000 genomes]
rs2911989	0.90[AFR][1000 genomes]
rs2911992	0.82[EUR][1000 genomes]
rs2912083	0.87[AFR][1000 genomes]
rs2928614	0.87[AFR][1000 genomes]
rs2928616	0.90[AFR][1000 genomes]
rs2928617	0.81[EUR][1000 genomes]
rs3780087	0.90[ASN][1000 genomes]
rs6559177	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs992812	0.91[ASN][1000 genomes]
rs992813	0.90[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:67 , 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	chr8:6548600-6561800	Weak transcription	Fetal Thymus	thymus
7	chr8:6548600-6563800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr8:6548600-6564400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr8:6548800-6564200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr8:6549400-6564000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr8:6549400-6565000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr8:6549600-6563600	Weak transcription	Primary T cells from cord blood	blood
13	chr8:6550400-6561600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr8:6551800-6561200	Weak transcription	A549	lung
15	chr8:6552000-6563600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr8:6552000-6565200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr8:6552000-6565200	Weak transcription	Pancreas	Pancrea
18	chr8:6552200-6563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr8:6552200-6564000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr8:6552400-6563600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr8:6552600-6563400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:6553000-6563800	Weak transcription	Gastric	stomach
23	chr8:6553400-6564200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr8:6553600-6561800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr8:6554200-6563800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr8:6554200-6565200	Weak transcription	Aorta	Aorta
27	chr8:6554600-6565000	Weak transcription	Brain Hippocampus Middle	brain
28	chr8:6554800-6564600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:6555200-6563600	Weak transcription	Fetal Intestine Large	intestine
30	chr8:6555600-6564400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr8:6555600-6565200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:6555800-6563600	Weak transcription	Fetal Intestine Small	intestine
33	chr8:6556200-6563200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr8:6556200-6563600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr8:6556200-6564200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr8:6556800-6561200	Weak transcription	K562	blood
37	chr8:6556800-6561800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr8:6556800-6564000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr8:6556800-6564000	Weak transcription	Fetal Muscle Leg	muscle
40	chr8:6557000-6563800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr8:6557000-6565200	Weak transcription	Lung	lung
42	chr8:6557200-6561800	Weak transcription	Fetal Stomach	stomach
43	chr8:6557400-6561200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr8:6557400-6563600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr8:6557400-6563800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr8:6557400-6563800	Weak transcription	Placenta	Placenta
47	chr8:6557400-6564200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr8:6557400-6565000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr8:6558000-6565000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr8:6558200-6563600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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