Variant report

Variant	rs12748054
Chromosome Location	chr1:180892952-180892953
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:180892093-180893077	H1-hESC	embryonic stem cell:	n/a	n/a
2	NFIC	chr1:180892117-180893132	ECC-1	luminal epithelium:	n/a	n/a
3	TBP	chr1:180892205-180893001	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:180891954-180893190	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr1:180892061-180892978	ECC-1	luminal epithelium:	n/a	n/a
6	CTBP2	chr1:180892209-180893022	H1-hESC	embryonic stem cell:	n/a	n/a
7	EP300	chr1:180892077-180893042	ECC-1	luminal epithelium:	n/a	n/a
8	GATA1	chr1:180892696-180893607	PBDE	blood:	n/a	n/a
9	CHD2	chr1:180892771-180892966	Hela-S3	cervix:	n/a	n/a
10	TEAD4	chr1:180892093-180893102	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr1:180892446-180892953	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr1:180892170-180893017	H1-hESC	embryonic stem cell:	n/a	n/a
13	TCF12	chr1:180892054-180893071	ECC-1	luminal epithelium:	n/a	n/a
14	SIN3A	chr1:180892009-180892955	H1-hESC	embryonic stem cell:	n/a	n/a
15	NFIC	chr1:180892128-180893082	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180892623..180894701-chr1:180898056..180900567,2	MCF-7	breast:
2	chr1:180875236..180876989-chr1:180891969..180894800,2	K562	blood:
3	chr1:180469860..180472607-chr1:180890916..180893412,2	K562	blood:
4	chr1:180889227..180893527-chr1:180894947..180897442,3	MCF-7	breast:
5	chr1:180891831..180893938-chr1:180895346..180897268,3	K562	blood:
6	chr1:180892738..180895948-chr1:181056431..181059504,3	K562	blood:
7	chr1:180885638..180890175-chr1:180892218..180894358,4	MCF-7	breast:

No data

Variant related genes	Relation type
KIAA1614	TF binding region
ENSG00000162783	Chromatin interaction
ENSG00000135847	Chromatin interaction
ENSG00000225857	Chromatin interaction
ENSG00000135835	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11581837	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11582550	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11584360	0.91[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11587899	0.96[CEU][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12735084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12753478	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13374657	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv872579	chr1:180881148-180931508	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1001918	chr1:180886750-180908005	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180882400-180894600	Weak transcription	Pancreas	Pancrea
2	chr1:180882600-180894000	Weak transcription	Brain Substantia Nigra	brain
3	chr1:180882800-180894400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:180883000-180894600	Weak transcription	Right Ventricle	heart
5	chr1:180883000-180894800	Weak transcription	Colonic Mucosa	Colon
6	chr1:180883200-180894200	Weak transcription	Brain Angular Gyrus	brain
7	chr1:180883600-180894200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:180883600-180894200	Weak transcription	Fetal Lung	lung
9	chr1:180883600-180894800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:180883600-180895000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:180885800-180895000	Weak transcription	NHLF	lung
12	chr1:180886000-180911000	Enhancers	Fetal Thymus	thymus
13	chr1:180887400-180893000	Strong transcription	Fetal Stomach	stomach
14	chr1:180887600-180915800	Weak transcription	Osteobl	bone
15	chr1:180888200-180894200	Weak transcription	Left Ventricle	heart
16	chr1:180888400-180894400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:180888400-180897600	Weak transcription	Aorta	Aorta
18	chr1:180888600-180917200	Weak transcription	Gastric	stomach
19	chr1:180889200-180894800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:180890400-180895600	Enhancers	Thymus	Thymus
21	chr1:180890400-180898200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:180890600-180893400	Strong transcription	Ovary	ovary
23	chr1:180890600-180898000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:180890800-180893600	Genic enhancers	Fetal Muscle Leg	muscle
25	chr1:180890800-180898200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:180890800-180898600	Enhancers	Placenta	Placenta
27	chr1:180891000-180894000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:180891000-180897800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr1:180891200-180893200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:180891200-180893200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:180891200-180893200	Enhancers	HSMMtube	muscle
32	chr1:180891200-180893600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:180891200-180894200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:180891200-180894200	Weak transcription	Fetal Brain Male	brain
35	chr1:180891400-180893000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr1:180891400-180896600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:180891600-180893200	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr1:180891600-180893200	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr1:180891600-180901000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:180891800-180893000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:180891800-180893000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:180891800-180893400	Enhancers	HSMM	muscle
43	chr1:180891800-180893800	Enhancers	Fetal Brain Female	brain
44	chr1:180891800-180895200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:180891800-180898200	Enhancers	Fetal Muscle Trunk	muscle
46	chr1:180892000-180893000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
47	chr1:180892000-180893000	Enhancers	Fetal Intestine Small	intestine
48	chr1:180892000-180893200	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr1:180892000-180893200	Enhancers	Fetal Heart	heart
50	chr1:180892200-180893000	Enhancers	Muscle Satellite Cultured Cells	--

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