Variant report

Variant	rs6493886
Chromosome Location	chr15:57027079-57027080
allele	A/G
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	KAP1	chr15:57025728-57027111	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:57023111..57027218-chr15:57209095..57213054,4	K562	blood:
2	chr15:56534684..56537162-chr15:57025486..57027553,2	MCF-7	breast:
3	chr15:57022824..57027100-chr15:57611258..57614634,3	K562	blood:
4	chr15:56997588..56999927-chr15:57024317..57027282,2	K562	blood:

Variant related genes	Relation type
ZNF280D	TF binding region
ENSG00000140262	Chromatin interaction
ENSG00000151575	Chromatin interaction
ENSG00000260172	Chromatin interaction
ENSG00000137871	Chromatin interaction
ENSG00000181827	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10518871	0.94[CEU][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10518878	0.85[EUR][1000 genomes]
rs11071290	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11852822	0.84[EUR][1000 genomes]
rs11856432	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1441236	0.82[CEU][hapmap]
rs1647392	0.82[CEU][hapmap]
rs16977079	0.82[ASN][1000 genomes]
rs2128171	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2278613	0.82[CEU][hapmap]
rs28437201	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6493882	0.94[CEU][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6493892	0.82[EUR][1000 genomes]
rs6493893	0.82[CEU][hapmap]
rs7164095	0.94[CEU][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs7166876	0.88[EUR][1000 genomes]
rs7173137	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7175191	0.88[CEU][hapmap]
rs7178196	0.82[EUR][1000 genomes]
rs7182691	0.81[EUR][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	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	nsv569576	chr15:57012816-57126917	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6493886	TEX9	cis	parietal	SCAN
rs6493886	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57026000-57027200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
2	chr15:57026000-57028600	Weak transcription	HUVEC	blood vessel
3	chr15:57026000-57029400	Weak transcription	NH-A	brain
4	chr15:57026200-57028200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:57026200-57028400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:57026200-57028600	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:57026200-57029000	Weak transcription	Small Intestine	intestine
8	chr15:57026200-57029200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:57026200-57029200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:57026200-57029200	Weak transcription	Ovary	ovary
11	chr15:57026200-57029600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:57026200-57032400	Weak transcription	Pancreas	Pancrea
13	chr15:57026400-57027200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:57026400-57027600	Weak transcription	HepG2	liver
15	chr15:57026400-57027800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:57026400-57027800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:57026400-57028200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:57026400-57029000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:57026400-57029200	Enhancers	K562	blood
20	chr15:57026400-57029400	Weak transcription	Fetal Kidney	kidney
21	chr15:57026800-57027200	Weak transcription	Fetal Stomach	stomach
22	chr15:57026800-57028200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:57026800-57029000	Weak transcription	Fetal Thymus	thymus
24	chr15:57026800-57030000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:57027000-57027600	Weak transcription	Placenta	Placenta
26	chr15:57027000-57028600	Weak transcription	Hela-S3	cervix

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