Variant report

Variant	rs6097805
Chromosome Location	chr20:52768496-52768497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:95288063..95290182-chr20:52767433..52769417,2	MCF-7	breast:
2	chr17:56707032..56710436-chr20:52766357..52772037,9	MCF-7	breast:
3	chr20:52766754..52768697-chr8:144820849..144823437,2	MCF-7	breast:
4	chr20:52768122..52769040-chr20:52811641..52812560,3	MCF-7	breast:
5	chr17:59484836..59487609-chr20:52766414..52769329,2	MCF-7	breast:
6	chr17:56706368..56709577-chr20:52768047..52771187,3	MCF-7	breast:
7	chr17:56735424..56738028-chr20:52767765..52769885,2	MCF-7	breast:
8	chr17:56735238..56739776-chr20:52762796..52768683,6	MCF-7	breast:
9	chr17:59484574..59486757-chr20:52768086..52769759,2	MCF-7	breast:
10	chr17:59489837..59492539-chr20:52768488..52770171,2	MCF-7	breast:
11	chr17:57970442..57972111-chr20:52766595..52769433,2	MCF-7	breast:
12	chr20:52211908..52215151-chr20:52766884..52771883,4	MCF-7	breast:
13	chr20:52739905..52740841-chr20:52768331..52768949,5	MCF-7	breast:
14	chr20:52740259..52740856-chr20:52768240..52768937,2	MCF-7	breast:
15	chr20:52768317..52770399-chr20:52774857..52777374,2	K562	blood:
16	chr20:52768371..52769040-chr20:52811641..52812154,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000108443	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000203499	Chromatin interaction
ENSG00000266826	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1570669	0.91[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1570670	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1985565	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274130	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274132	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2296237	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2296238	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2296239	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2296240	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787553	0.91[ASN][1000 genomes]
rs4809956	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs4809957	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4811494	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56808842	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59895069	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6022985	0.84[AMR][1000 genomes]
rs6091824	0.91[ASN][1000 genomes]
rs6091825	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6091826	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6097806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097807	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];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097810	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs751087	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751089	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs912505	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs927648	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs927651	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs927652	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv912945	chr20:52746724-52772741	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv912946	chr20:52758416-52772741	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
5	nsv1063981	chr20:52765317-52776613	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2762085	chr20:52765329-52776625	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv586281	chr20:52765349-52771171	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1058882	chr20:52765979-52794372	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6097805	NFATC2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52758600-52768800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:52766000-52768800	Weak transcription	NHEK	skin
3	chr20:52766400-52768600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr20:52766400-52768800	Weak transcription	HepG2	liver
5	chr20:52766800-52768600	Enhancers	A549	lung
6	chr20:52768200-52769400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr20:52768400-52768800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr20:52768400-52769800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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