Variant report

Variant	rs7164742
Chromosome Location	chr15:57209618-57209619
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	POLR2A	chr15:57209256-57213061	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:57209602-57209802	MCF10A-Er-Src	breast:	n/a	n/a
3	JUN	chr15:57208971-57209668	K562	blood:	n/a	chr15:57209238-57209246 chr15:57209099-57209108
4	MAX	chr15:57209546-57212889	A549	lung:	n/a	chr15:57210744-57210754
5	E2F6	chr15:57209607-57212068	K562	blood:	n/a	chr15:57211231-57211238 chr15:57210776-57210785 chr15:57211230-57211239 chr15:57210743-57210752 chr15:57211231-57211238 chr15:57211095-57211105 chr15:57211309-57211318 chr15:57211231-57211238 chr15:57211926-57211938 chr15:57210740-57210752
6	MTA3	chr15:57209616-57211158	GM12878	blood:	n/a	n/a
7	MYC	chr15:57209603-57212933	A549	lung:	n/a	chr15:57210744-57210754

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57023111..57027218-chr15:57209095..57213054,4	K562	blood:

Variant related genes	Relation type
TCF12	TF binding region
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11630965	0.86[ASN][1000 genomes]
rs11856338	0.91[CEU][hapmap];0.90[TSI][hapmap]
rs12437976	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440219	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12902058	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs12906025	0.95[CEU][hapmap];0.90[TSI][hapmap]
rs1625176	0.85[TSI][hapmap]
rs1631079	0.85[TSI][hapmap]
rs1642927	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs1642940	0.81[CEU][hapmap]
rs1652738	0.85[TSI][hapmap]
rs1652739	0.85[TSI][hapmap]
rs190039	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs1963831	0.90[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1975092	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2111890	0.91[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs2116067	0.94[ASN][1000 genomes]
rs2116068	0.93[ASN][1000 genomes]
rs213155	0.91[CEU][hapmap];0.90[TSI][hapmap]
rs213163	0.87[TSI][hapmap]
rs2252289	0.85[TSI][hapmap]
rs2435905	0.85[TSI][hapmap]
rs2464427	0.82[TSI][hapmap]
rs2470081	0.85[TSI][hapmap]
rs2543675	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs2566840	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2566844	0.85[TSI][hapmap]
rs2566856	0.85[TSI][hapmap]
rs2585076	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs2733187	0.85[TSI][hapmap]
rs2957576	0.85[TSI][hapmap]
rs2957578	0.85[TSI][hapmap]
rs34373044	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4581646	0.97[ASN][1000 genomes]
rs4774246	0.95[CEU][hapmap];0.83[TSI][hapmap]
rs4774247	0.80[EUR][1000 genomes]
rs4774900	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7162730	0.82[EUR][1000 genomes]
rs7168945	0.95[CEU][hapmap]
rs8031788	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9806712	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription 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	21 gene(s)	inside rSNPs	diseases
7	esv3419108	chr15:57209560-57212908	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7164742	hCT1971351.1	cis	multi-tissue	Pritchard
rs7164742	TCF12	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57206000-57209800	Weak transcription	HSMM	muscle
2	chr15:57207000-57209800	Weak transcription	Aorta	Aorta
3	chr15:57208400-57209800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:57208600-57210000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:57209000-57209800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:57209000-57209800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr15:57209000-57209800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr15:57209000-57209800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:57209000-57209800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:57209000-57209800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr15:57209000-57209800	Enhancers	Liver	Liver
12	chr15:57209000-57209800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr15:57209000-57209800	Enhancers	Placenta	Placenta
14	chr15:57209000-57209800	Enhancers	Gastric	stomach
15	chr15:57209000-57209800	Enhancers	Stomach Mucosa	stomach
16	chr15:57209000-57210000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr15:57209000-57210200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:57209000-57210200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr15:57209000-57210200	Enhancers	Spleen	Spleen
20	chr15:57209000-57210200	Flanking Active TSS	K562	blood
21	chr15:57209000-57210400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:57209000-57210400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:57209000-57210400	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr15:57209200-57209800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:57209200-57209800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:57209200-57209800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:57209200-57209800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:57209200-57209800	Enhancers	Primary B cells from peripheral blood	blood
29	chr15:57209200-57209800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:57209200-57209800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:57209200-57209800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:57209200-57209800	Enhancers	Fetal Stomach	stomach
33	chr15:57209200-57210000	Transcr. at gene 5' and 3'	Fetal Lung	lung
34	chr15:57209200-57210000	Enhancers	Placenta Amnion	Placenta Amnion
35	chr15:57209200-57210000	Flanking Active TSS	A549	lung
36	chr15:57209200-57210200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr15:57209200-57210200	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr15:57209200-57210200	Flanking Active TSS	Fetal Heart	heart
39	chr15:57209200-57210200	Enhancers	Small Intestine	intestine
40	chr15:57209200-57210200	Flanking Active TSS	Osteobl	bone
41	chr15:57209200-57210600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:57209200-57210600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr15:57209200-57212200	Active TSS	Stomach Smooth Muscle	stomach
44	chr15:57209200-57213000	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr15:57209200-57213000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:57209400-57209800	Active TSS	Pancreas	Pancrea
47	chr15:57209400-57209800	Active TSS	GM12878-XiMat	blood
48	chr15:57209400-57210200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
49	chr15:57209400-57210200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
50	chr15:57209400-57210200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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