Variant report

Variant	rs11896000
Chromosome Location	chr2:20646109-20646110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:20646048-20648294	A549	lung:	n/a	chr2:20646693-20646703
2	POLR2A	chr2:20646043-20652533	HUVEC	blood vessel:	n/a	n/a
3	SIX5	chr2:20646086-20647084	A549	lung:	n/a	n/a
4	POLR2A	chr2:20645918-20651649	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr2:20645370-20646215	PFSK-1	brain:	n/a	n/a
6	HEY1	chr2:20645541-20650862	HepG2	liver:	n/a	chr2:20646608-20646623
7	POLR2A	chr2:20646006-20652601	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:20645948-20651806	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr2:20645989-20652401	IMR90	lung:	n/a	n/a
10	ZBTB7A	chr2:20646057-20647475	ECC-1	luminal epithelium:	n/a	chr2:20646810-20646819
11	MAZ	chr2:20646022-20649127	IMR90	lung:	n/a	chr2:20646693-20646703
12	POLR2A	chr2:20645960-20646224	HUVEC	blood vessel:	n/a	n/a
13	RUNX3	chr2:20646024-20647695	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:20645976-20650968	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr2:20646012-20646260	HCT-116	colon:	n/a	n/a
16	POLR2A	chr2:20645961-20646326	HCT-116	colon:	n/a	n/a
17	POLR2A	chr2:20645826-20652982	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr2:20645973-20651501	HepG2	liver:	n/a	n/a
19	BCL3	chr2:20645995-20647064	A549	lung:	n/a	chr2:20646612-20646625 chr2:20646174-20646183
20	CHD2	chr2:20646081-20647929	Hela-S3	cervix:	n/a	n/a
21	REST	chr2:20645943-20648189	H1-neurons	neurons:	n/a	chr2:20646622-20646640 chr2:20646684-20646697 chr2:20646625-20646638
22	CHD1	chr2:20645950-20651592	IMR90	lung:	n/a	n/a
23	POLR2A	chr2:20645938-20651588	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr2:20645955-20650956	HepG2	liver:	n/a	n/a
25	HCFC1	chr2:20645912-20651140	Hela-S3	cervix:	n/a	n/a
26	RFX5	chr2:20645844-20651474	SK-N-SH	brain:	n/a	chr2:20646718-20646727
27	TCF12	chr2:20645888-20648991	A549	lung:	n/a	chr2:20646117-20646124
28	POLR2A	chr2:20646061-20651465	Hela-S3	cervix:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20646044..20646619-chr6:13328688..13329216,2	HCT-116	colon:
2	chr2:20549379..20553875-chr2:20644345..20648832,13	MCF-7	breast:
3	chr2:20633992..20655025-chr2:20829429..20854651,127	MCF-7	breast:
4	chr2:20645830..20649178-chr2:20802657..20807893,7	MCF-7	breast:
5	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
6	chr2:20644186..20651576-chr2:20790196..20799394,18	MCF-7	breast:
7	chr2:20645492..20647330-chr7:139044300..139046201,2	MCF-7	breast:
8	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
9	chr2:20592640..20602218-chr2:20644635..20652468,15	MCF-7	breast:
10	chr2:20645526..20651779-chr2:20782666..20787622,12	MCF-7	breast:
11	chr16:68268541..68270954-chr2:20645662..20648627,2	MCF-7	breast:
12	chr2:20645423..20650748-chr2:20698837..20705480,9	MCF-7	breast:
13	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:
14	chr2:20645482..20647454-chr9:137444146..137446326,2	MCF-7	breast:
15	chr2:20548847..20552407-chr2:20645405..20649585,5	MCF-7	breast:

No data

Variant related genes	Relation type
RHOB	TF binding region
ENSG00000228950	TF binding region
ENSG00000212171	Chromatin interaction
ENSG00000145979	Chromatin interaction
ENSG00000252216	Chromatin interaction
ENSG00000233416	Chromatin interaction
ENSG00000269976	Chromatin interaction
ENSG00000231948	Chromatin interaction
ENSG00000273391	Chromatin interaction
ENSG00000227150	Chromatin interaction
ENSG00000118960	Chromatin interaction
ENSG00000103067	Chromatin interaction
ENSG00000146963	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000227047	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11889962	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342099	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv455830	chr2:20621404-20659862	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv581166	chr2:20621404-20659862	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
3	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
8	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20639600-20646200	Weak transcription	HMEC	breast
2	chr2:20642000-20646200	Weak transcription	K562	blood
3	chr2:20643200-20646200	Enhancers	NHDF-Ad	bronchial
4	chr2:20643400-20646200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:20643600-20650000	Active TSS	Right Atrium	heart
6	chr2:20644000-20646200	Weak transcription	Fetal Lung	lung
7	chr2:20644400-20646200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:20644400-20646400	Flanking Active TSS	HUVEC	blood vessel
9	chr2:20644600-20646200	Weak transcription	Fetal Kidney	kidney
10	chr2:20644600-20646200	Weak transcription	Small Intestine	intestine
11	chr2:20644600-20647000	Active TSS	Right Ventricle	heart
12	chr2:20644600-20650000	Active TSS	Psoas Muscle	Psoas
13	chr2:20644800-20646200	Enhancers	Lung	lung
14	chr2:20644800-20646400	Enhancers	Spleen	Spleen
15	chr2:20645000-20646200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
16	chr2:20645000-20650600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr2:20645200-20647200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:20645400-20647400	Active TSS	Brain Substantia Nigra	brain
19	chr2:20645400-20647600	Active TSS	Aorta	Aorta
20	chr2:20645400-20648600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr2:20645600-20646200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
22	chr2:20645600-20647200	Active TSS	Brain Hippocampus Middle	brain
23	chr2:20645600-20647200	Active TSS	Stomach Smooth Muscle	stomach
24	chr2:20645600-20647400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr2:20645600-20647400	Active TSS	Colon Smooth Muscle	Colon
26	chr2:20645600-20647400	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr2:20645600-20648400	Active TSS	Brain Anterior Caudate	brain
28	chr2:20645600-20650000	Active TSS	Brain Angular Gyrus	brain
29	chr2:20646000-20646200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:20646000-20646200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:20646000-20646200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:20646000-20646200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:20646000-20646200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:20646000-20646200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:20646000-20646200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:20646000-20646200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:20646000-20646200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:20646000-20646200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
39	chr2:20646000-20646200	Bivalent Enhancer	Primary T cells from cord blood	blood
40	chr2:20646000-20646200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr2:20646000-20646200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
42	chr2:20646000-20646200	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:20646000-20646200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
44	chr2:20646000-20646200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:20646000-20646200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
46	chr2:20646000-20646200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
47	chr2:20646000-20646200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:20646000-20646200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
49	chr2:20646000-20646200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr2:20646000-20646200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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