Variant report

Variant	rs7954816
Chromosome Location	chr12:11709083-11709084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:11706778-11710160	GM12891	blood:	n/a	n/a
2	POU2F2	chr12:11708523-11709468	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:11708072-11709584	GM12878	blood:	n/a	n/a
4	PML	chr12:11708530-11709424	GM12878	blood:	n/a	n/a
5	NFIC	chr12:11708461-11709316	GM12878	blood:	n/a	n/a
6	GATA3	chr12:11708624-11709250	MCF-7	breast:	n/a	n/a
7	POLR2A	chr12:11708037-11709575	GM12878	blood:	n/a	n/a
8	TAF1	chr12:11708998-11709442	GM12891	blood:	n/a	n/a
9	POLR2A	chr12:11706813-11709512	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:11708141-11709606	GM12891	blood:	n/a	n/a
11	KAP1	chr12:11708457-11709394	U2OS	brain:	n/a	n/a
12	GATA3	chr12:11708620-11709317	MCF-7	breast:	n/a	n/a
13	GATA3	chr12:11708534-11709167	MCF-7	breast:	n/a	n/a
14	POLR2A	chr12:11708084-11710112	GM12891	blood:	n/a	n/a
15	POLR2A	chr12:11708124-11709493	GM12891	blood:	n/a	n/a
16	TBP	chr12:11708607-11709482	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:11708626-11709571	GM12878	blood:	n/a	n/a
18	RUNX3	chr12:11708558-11709478	GM12878	blood:	n/a	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ETV6-1	chr12:11708189-11710150	ENSG00000247157
2	lnc-ETV6-1	chr12:11708189-11710150	NR_033890

No data

Variant related genes	Relation type
ENSG00000247157	TF binding region
ENSG00000256237	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10491979	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491981	0.90[EUR][1000 genomes]
rs12304175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307843	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16935010	0.93[EUR][1000 genomes]
rs16935013	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16935135	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745379	0.93[EUR][1000 genomes]
rs17745415	0.90[EUR][1000 genomes]
rs17818016	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[EUR][1000 genomes]
rs17818022	0.93[EUR][1000 genomes]
rs1795551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57529731	0.93[EUR][1000 genomes]
rs61472986	0.93[EUR][1000 genomes]
rs7302311	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73286605	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73286618	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972594	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975032	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs969769	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv469112	chr12:11575570-11711690	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv557573	chr12:11575570-11711690	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11706800-11709400	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr12:11706800-11709600	Enhancers	Dnd41	blood
3	chr12:11708000-11709200	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr12:11708000-11709400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr12:11708000-11709400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:11708000-11709600	Enhancers	Fetal Thymus	thymus
7	chr12:11708200-11709400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:11708200-11709600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:11708200-11709800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr12:11708400-11709200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:11708400-11709200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr12:11708400-11709600	Flanking Active TSS	GM12878-XiMat	blood
13	chr12:11708400-11709800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:11708400-11709800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr12:11708400-11710200	Active TSS	Aorta	Aorta
16	chr12:11708600-11709200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr12:11708600-11709200	Enhancers	Fetal Intestine Large	intestine
18	chr12:11708600-11709200	Flanking Active TSS	Fetal Intestine Small	intestine
19	chr12:11708600-11709200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr12:11708600-11709200	Flanking Active TSS	Rectal Smooth Muscle	rectum
21	chr12:11708600-11709200	Enhancers	Thymus	Thymus
22	chr12:11708600-11709400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:11708600-11709400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr12:11708600-11709400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr12:11708600-11709400	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr12:11708600-11709400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr12:11708600-11710200	Active TSS	Stomach Smooth Muscle	stomach
28	chr12:11708800-11709200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:11708800-11709200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr12:11708800-11709200	Flanking Active TSS	Colonic Mucosa	Colon
31	chr12:11708800-11709200	Enhancers	Esophagus	oesophagus
32	chr12:11708800-11709200	Flanking Active TSS	Stomach Mucosa	stomach
33	chr12:11708800-11709200	Enhancers	K562	blood
34	chr12:11708800-11709400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr12:11708800-11709400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr12:11708800-11709400	Bivalent/Poised TSS	A549	lung
37	chr12:11708800-11709600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:11708800-11709600	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr12:11709000-11709200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr12:11709000-11709200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:11709000-11709200	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr12:11709000-11709200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:11709000-11709200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:11709000-11709200	Flanking Active TSS	Pancreas	Pancrea
45	chr12:11709000-11709400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:11709000-11709400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:11709000-11709400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:11709000-11709400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr12:11709000-11709400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:11709000-11709400	Active TSS	Gastric	stomach

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