Variant report

Variant	rs7969190
Chromosome Location	chr12:116970692-116970693
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	YY1	chr12:116970144-116970701	GM12878	blood:	n/a	chr12:116970370-116970382
2	CUX1	chr12:116970303-116970752	K562	blood:	n/a	n/a
3	MYC	chr12:116970397-116972371	K562	blood:	n/a	chr12:116970552-116970561 chr12:116971137-116971147 chr12:116971149-116971158
4	MAX	chr12:116970339-116971596	K562	blood:	n/a	chr12:116970552-116970561 chr12:116971137-116971147 chr12:116971149-116971158
5	YY1	chr12:116970172-116970693	H1-hESC	embryonic stem cell:	n/a	chr12:116970370-116970382
6	REST	chr12:116970601-116973294	H1-neurons	neurons:	n/a	n/a
7	TCF12	chr12:116970532-116972572	A549	lung:	n/a	n/a
8	MAX	chr12:116970339-116972111	A549	lung:	n/a	chr12:116970552-116970561 chr12:116971137-116971147 chr12:116971149-116971158
9	MYC	chr12:116970392-116972000	K562	blood:	n/a	chr12:116970552-116970561 chr12:116971137-116971147 chr12:116971149-116971158
10	POLR2A	chr12:116970347-116971938	HCT-116	colon:	n/a	n/a
11	MAZ	chr12:116970669-116972872	IMR90	lung:	n/a	chr12:116971137-116971147 chr12:116971149-116971158
12	SP1	chr12:116970318-116972445	A549	lung:	n/a	chr12:116971134-116971146 chr12:116971155-116971167 chr12:116971183-116971193 chr12:116971135-116971145 chr12:116971183-116971192 chr12:116971155-116971167 chr12:116971136-116971145 chr12:116971157-116971166 chr12:116971182-116971194 chr12:116971182-116971193 chr12:116971156-116971165 chr12:116971182-116971194 chr12:116971135-116971144 chr12:116971135-116971145 chr12:116971134-116971146 chr12:116971862-116971873 chr12:116971184-116971193 chr12:116971207-116971217 chr12:116971135-116971149 chr12:116971135-116971144 chr12:116971183-116971193 chr12:116971156-116971165 chr12:116971183-116971192 chr12:116971873-116971884
13	E2F6	chr12:116970476-116971427	K562	blood:	n/a	chr12:116971136-116971145 chr12:116971184-116971193 chr12:116971179-116971189
14	EP300	chr12:116970682-116971825	A549	lung:	n/a	n/a
15	POLR2A	chr12:116970419-116972701	Raji	blood:	n/a	n/a
16	ZNF384	chr12:116970133-116970725	K562	blood:	n/a	n/a
17	MAX	chr12:116970416-116971511	NB4	blood:	n/a	chr12:116970552-116970561 chr12:116971137-116971147 chr12:116971149-116971158
18	E2F6	chr12:116970328-116971582	A549	lung:	n/a	chr12:116971136-116971145 chr12:116971184-116971193 chr12:116971179-116971189
19	MAX	chr12:116970227-116972669	A549	lung:	n/a	chr12:116970552-116970561 chr12:116971137-116971147 chr12:116971149-116971158

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:116968953..116973759-chr12:116995509..116998903,7	K562	blood:
2	chr12:116712747..116717142-chr12:116969029..116973550,6	MCF-7	breast:

Variant related genes	Relation type
LINC00173	TF binding region
ENSG00000123066	Chromatin interaction
ENSG00000171471	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10774871	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10774872	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10850662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10850663	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11068062	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068070	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11068075	0.84[ASN][1000 genomes]
rs11609040	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11609872	0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11610226	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11615960	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394801	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1394802	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2047952	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2089222	0.83[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2102294	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2893685	0.82[ASN][1000 genomes]
rs60521218	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6490075	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6490076	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7297552	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7300418	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7304300	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7315385	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7954181	0.99[ASN][1000 genomes]
rs7961538	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7969566	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972701	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976256	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899540	chr12:116920503-116999861	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:116962800-116970800	Weak transcription	Aorta	Aorta
2	chr12:116963800-116970800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:116963800-116970800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:116964000-116971000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:116964200-116970800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:116966800-116970800	Weak transcription	HUVEC	blood vessel
7	chr12:116967000-116970800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:116967200-116970800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:116967200-116970800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:116967200-116970800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:116967200-116970800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:116967200-116970800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:116967200-116970800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:116967200-116970800	Weak transcription	NH-A	brain
15	chr12:116967200-116971400	Weak transcription	HSMMtube	muscle
16	chr12:116967400-116970800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:116968200-116970800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:116970000-116970800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:116970000-116971200	Enhancers	Gastric	stomach
20	chr12:116970200-116970800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr12:116970200-116970800	Enhancers	Thymus	Thymus
22	chr12:116970400-116970800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
23	chr12:116970400-116970800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:116970400-116970800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr12:116970400-116970800	Enhancers	Primary B cells from cord blood	blood
26	chr12:116970400-116970800	Enhancers	Primary B cells from peripheral blood	blood
27	chr12:116970400-116970800	Enhancers	Primary hematopoietic stem cells	blood
28	chr12:116970400-116970800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:116970400-116970800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:116970400-116970800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:116970400-116970800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:116970400-116970800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:116970400-116970800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:116970400-116970800	Bivalent Enhancer	Adipose Nuclei	Adipose
35	chr12:116970400-116970800	Enhancers	Brain Anterior Caudate	brain
36	chr12:116970400-116970800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:116970400-116970800	Enhancers	Brain Substantia Nigra	brain
38	chr12:116970400-116970800	Enhancers	Colonic Mucosa	Colon
39	chr12:116970400-116970800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr12:116970400-116970800	Enhancers	Fetal Brain Male	brain
41	chr12:116970400-116970800	Enhancers	Fetal Intestine Large	intestine
42	chr12:116970400-116970800	Enhancers	Fetal Intestine Small	intestine
43	chr12:116970400-116970800	Enhancers	Fetal Muscle Leg	muscle
44	chr12:116970400-116970800	Enhancers	Fetal Stomach	stomach
45	chr12:116970400-116970800	Enhancers	Fetal Thymus	thymus
46	chr12:116970400-116970800	Enhancers	Ovary	ovary
47	chr12:116970400-116970800	Enhancers	Pancreas	Pancrea
48	chr12:116970400-116970800	Enhancers	Psoas Muscle	Psoas
49	chr12:116970400-116970800	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr12:116970400-116970800	Enhancers	Rectal Smooth Muscle	rectum

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