Variant report

Variant	rs4553444
Chromosome Location	chr12:64433445-64433446
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	TCF7L2	chr12:64433076-64433765	PANC-1	pancreas:	n/a	n/a
2	SIN3AK20	chr12:64433060-64433810	MCF-7	breast:	n/a	n/a
3	USF1	chr12:64433158-64433547	SK-N-SH_RA	brain:	n/a	n/a
4	NR2F2	chr12:64433116-64433847	MCF-7	breast:	n/a	chr12:64433561-64433576
5	FOXA1	chr12:64433366-64433644	T-47D	breast:	n/a	n/a
6	USF1	chr12:64433232-64433452	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOXA2	chr12:64433364-64433716	A549	lung:	n/a	n/a
8	POLR2A	chr12:64433213-64433779	PANC-1	pancreas:	n/a	n/a
9	FOXA2	chr12:64433326-64433741	A549	lung:	n/a	n/a
10	GATA3	chr12:64433258-64433788	MCF-7	breast:	n/a	chr12:64433524-64433532
11	KAP1	chr12:64432928-64433694	HEK293	kidney:	n/a	n/a
12	MYC	chr12:64433269-64433481	MCF10A-Er-Src	breast:	n/a	n/a
13	USF1	chr12:64433175-64433523	SK-N-SH_RA	brain:	n/a	n/a
14	TCF12	chr12:64433038-64433849	MCF-7	breast:	n/a	chr12:64433613-64433623
15	TCF12	chr12:64433136-64433892	A549	lung:	n/a	chr12:64433613-64433623
16	ZNF217	chr12:64433165-64433607	MCF-7	breast:	n/a	n/a
17	FOS	chr12:64433283-64433475	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr12:64433370-64433788	PANC-1	pancreas:	n/a	n/a
19	NR2F2	chr12:64433185-64433839	MCF-7	breast:	n/a	chr12:64433561-64433576

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64432833..64435222-chr12:64436511..64438802,2	MCF-7	breast:
2	chr12:64432506..64434524-chr12:64443772..64446923,3	MCF-7	breast:

Variant related genes	Relation type
SRGAP1	TF binding region
ENSG00000196935	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10444577	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10878102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1162788	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12228437	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1344400	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1378778	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1456046	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2168411	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2647908	0.85[ASN][1000 genomes]
rs28366579	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763134	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60987129	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6581529	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581530	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963940	0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7980267	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs990309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64418600-64456400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:64428800-64450800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:64430200-64439800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:64431200-64437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:64431800-64433800	Enhancers	Fetal Brain Male	brain
6	chr12:64432000-64466400	Weak transcription	Pancreas	Pancrea
7	chr12:64432200-64433600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr12:64432200-64433800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:64432400-64433600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:64432400-64433600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:64432400-64433600	Enhancers	Fetal Kidney	kidney
12	chr12:64432400-64433800	Enhancers	Fetal Brain Female	brain
13	chr12:64432400-64434000	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr12:64432400-64434000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr12:64432400-64434000	Enhancers	HUVEC	blood vessel
16	chr12:64432400-64434200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr12:64432400-64434200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr12:64432400-64434200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr12:64432400-64434400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr12:64432600-64433600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:64432600-64433600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:64432600-64433600	Enhancers	NHEK	skin
23	chr12:64432600-64433800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:64432600-64433800	Enhancers	Brain Angular Gyrus	brain
25	chr12:64432600-64433800	Flanking Active TSS	NHDF-Ad	bronchial
26	chr12:64432600-64434000	Enhancers	A549	lung
27	chr12:64432600-64434000	Enhancers	Osteobl	bone
28	chr12:64432600-64434400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:64432800-64433600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:64432800-64433800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:64432800-64433800	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr12:64432800-64433800	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr12:64432800-64434000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:64432800-64434000	Enhancers	Fetal Heart	heart
35	chr12:64432800-64434200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr12:64433000-64433600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:64433000-64433600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr12:64433000-64433600	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr12:64433000-64433600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:64433000-64433600	Active TSS	Duodenum Mucosa	Duodenum
41	chr12:64433000-64433600	Enhancers	Esophagus	oesophagus
42	chr12:64433000-64433600	Enhancers	Left Ventricle	heart
43	chr12:64433000-64433600	Enhancers	Psoas Muscle	Psoas
44	chr12:64433000-64433600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr12:64433000-64433600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr12:64433000-64433600	Flanking Active TSS	HMEC	breast
47	chr12:64433000-64433600	Enhancers	HSMM	muscle
48	chr12:64433000-64433800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr12:64433000-64433800	Enhancers	Fetal Intestine Small	intestine
50	chr12:64433000-64433800	Active TSS	Pancreatic Islets	Pancreatic Islet

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