Variant report

Variant	rs17197710
Chromosome Location	chr11:47225996-47225997
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	NFIC	chr11:47225939-47226633	SK-N-SH	brain:	n/a	n/a
2	TAL1	chr11:47225981-47226163	K562	blood:	n/a	chr11:47226059-47226077
3	GATA3	chr11:47225721-47226649	MCF-7	breast:	n/a	chr11:47226059-47226076 chr11:47226068-47226077
4	GATA3	chr11:47225827-47226306	T-47D	breast:	n/a	chr11:47226059-47226076 chr11:47226068-47226077
5	TEAD4	chr11:47225823-47226525	K562	blood:	n/a	n/a
6	CTCF	chr11:47225980-47226130	HEEpiC	esophagus:	n/a	n/a
7	EP300	chr11:47225906-47226182	K562	blood:	n/a	chr11:47226039-47226047
8	GATA3	chr11:47225852-47226674	SK-N-SH	brain:	n/a	chr11:47226059-47226076 chr11:47226068-47226077
9	RCOR1	chr11:47225875-47226185	K562	blood:	n/a	n/a
10	GATA3	chr11:47225687-47226588	MCF-7	breast:	n/a	chr11:47226059-47226076 chr11:47226068-47226077
11	GATA1	chr11:47225770-47226697	K562	blood:	n/a	chr11:47226059-47226076 chr11:47226068-47226077

No.	Distal block	Cell Line	Cell type
1	chr11:47223065..47227984-chr11:47233675..47238356,6	MCF-7	breast:
2	chr11:47205640..47208812-chr11:47225906..47229370,3	MCF-7	breast:
3	chr11:47211780..47213676-chr11:47225698..47227391,2	MCF-7	breast:
4	chr11:47203683..47208496-chr11:47223862..47228000,5	MCF-7	breast:
5	chr11:47219819..47221860-chr11:47224771..47227015,2	MCF-7	breast:
6	chr11:47214523..47217185-chr11:47223816..47226023,3	MCF-7	breast:

Variant related genes	Relation type
RN7SL772P	TF binding region
ENSG00000165912	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000243802	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs12573962	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs12574558	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12575296	0.81[ASN][1000 genomes]
rs12576461	0.81[ASN][1000 genomes]
rs12576690	0.81[ASN][1000 genomes]
rs12576751	0.81[ASN][1000 genomes]
rs12576831	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12576839	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12576935	0.84[ASN][1000 genomes]
rs12578030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197500	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17197619	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17790246	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17790306	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17790336	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17790342	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17790390	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17790420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3736101	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs3816724	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs41301449	0.81[ASN][1000 genomes]
rs4572092	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4647713	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647720	0.80[ASN][1000 genomes]
rs4647736	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4647759	0.81[ASN][1000 genomes]
rs55968738	0.87[ASN][1000 genomes]
rs57012996	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57964319	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59689332	0.87[ASN][1000 genomes]
rs60041842	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60088916	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60174717	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60201196	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60335739	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61142746	0.87[ASN][1000 genomes]
rs61896051	0.81[ASN][1000 genomes]
rs61896053	0.81[ASN][1000 genomes]
rs61896054	0.81[ASN][1000 genomes]
rs61896120	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61896121	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61896122	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61896124	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61896125	0.93[ASN][1000 genomes]
rs61896126	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61896131	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61896132	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897776	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897777	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897782	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897784	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897786	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61897788	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897791	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61897843	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61897851	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897852	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897853	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61897854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61897855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897856	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899284	0.87[ASN][1000 genomes]
rs61899285	0.87[ASN][1000 genomes]
rs61899293	0.87[ASN][1000 genomes]
rs61899294	0.87[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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17197710	PACSIN3	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47210200-47226000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:47223000-47226000	Weak transcription	HepG2	liver
3	chr11:47224400-47230200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr11:47225600-47226000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:47225600-47226000	Enhancers	Hela-S3	cervix
6	chr11:47225600-47226200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:47225600-47226200	Enhancers	NHEK	skin
8	chr11:47225600-47226800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:47225600-47227200	Enhancers	HMEC	breast
10	chr11:47225600-47227200	Enhancers	Osteobl	bone
11	chr11:47225800-47226200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:47225800-47226400	Enhancers	Stomach Mucosa	stomach
13	chr11:47225800-47226600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr11:47225800-47226600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr11:47225800-47226600	Enhancers	Stomach Smooth Muscle	stomach
16	chr11:47225800-47226600	Enhancers	A549	lung
17	chr11:47225800-47226600	Enhancers	NHDF-Ad	bronchial
18	chr11:47225800-47226800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr11:47225800-47226800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr11:47225800-47226800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:47225800-47226800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:47225800-47227000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:47225800-47227000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr11:47225800-47227200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr11:47225800-47227200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:47225800-47227200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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