Variant report

Variant	rs6097632
Chromosome Location	chr20:52464353-52464354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52464155..52466021-chr6:26123311..26126264,2	MCF-7	breast:
2	chr20:52455023..52457769-chr20:52462367..52464597,2	K562	blood:
3	chr20:52463703..52464414-chr3:62849444..62850124,2	MCF-7	breast:
4	chr20:52446291..52448679-chr20:52463374..52466298,2	K562	blood:
5	chr20:52464253..52464773-chr7:84783688..84784207,2	MCF-7	breast:
6	chr20:52462638..52464808-chr3:62850144..62851891,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180596	Chromatin interaction
ENSG00000180573	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10432728	0.88[ASN][1000 genomes]
rs4809941	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4809942	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4811476	0.84[ASN][1000 genomes]
rs6013809	0.81[JPT][hapmap]
rs6022786	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs6022793	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6064011	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6068688	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6068690	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6068691	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6097618	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs6123320	0.85[AMR][1000 genomes]
rs6126982	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6126985	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6126986	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720387	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases
5	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6097632	NFATC2	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52450400-52465200	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr20:52450600-52465200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr20:52452400-52465200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr20:52453600-52480200	Weak transcription	Small Intestine	intestine
5	chr20:52455000-52464800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr20:52456600-52468400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:52456600-52476200	Weak transcription	Gastric	stomach
8	chr20:52458400-52466200	Enhancers	Fetal Thymus	thymus
9	chr20:52458800-52465200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr20:52459000-52466600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr20:52459400-52464400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr20:52459400-52465200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr20:52459600-52468400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr20:52459600-52472600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr20:52462000-52464600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr20:52462400-52465000	Enhancers	HepG2	liver
17	chr20:52462600-52464400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr20:52462800-52468200	Weak transcription	Osteobl	bone
19	chr20:52463000-52468400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr20:52463000-52474000	Weak transcription	A549	lung
21	chr20:52463200-52464800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr20:52463200-52465200	Enhancers	Primary hematopoietic stem cells	blood
23	chr20:52463200-52465200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr20:52463200-52465200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr20:52463400-52464400	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr20:52463400-52464800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr20:52463400-52464800	Enhancers	Brain Anterior Caudate	brain
28	chr20:52463400-52465000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr20:52463600-52464400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr20:52463600-52464400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr20:52463600-52464400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr20:52463600-52464600	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr20:52463600-52464600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr20:52463600-52464600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr20:52463600-52465000	Enhancers	Brain Substantia Nigra	brain
36	chr20:52463600-52465000	Flanking Active TSS	GM12878-XiMat	blood
37	chr20:52463800-52464400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr20:52463800-52464400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr20:52463800-52464400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr20:52463800-52464400	Enhancers	Fetal Lung	lung
41	chr20:52463800-52464600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr20:52463800-52464600	Enhancers	Brain Germinal Matrix	brain
43	chr20:52464000-52464400	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr20:52464000-52464400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr20:52464000-52464400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr20:52464000-52464400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr20:52464000-52464400	Flanking Active TSS	Dnd41	blood
48	chr20:52464000-52464400	Enhancers	HSMM	muscle
49	chr20:52464000-52464600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr20:52464200-52464400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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