Variant report

Variant	rs6097618
Chromosome Location	chr20:52448936-52448937
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57911189..57914106-chr20:52447367..52449133,2	MCF-7	breast:
2	chr20:52448530..52449144-chr20:57359341..57360238,2	MCF-7	breast:
3	chr20:52447680..52450529-chr3:63838228..63840003,2	MCF-7	breast:
4	chr17:57917840..57922874-chr20:52444092..52449259,5	MCF-7	breast:
5	chr20:52444427..52449219-chr20:55839929..55843430,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2215402	0.81[CEU][hapmap]
rs4809941	0.88[CEU][hapmap]
rs4809942	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs6013809	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs6022758	0.81[CEU][hapmap]
rs6022760	0.81[CEU][hapmap]
rs6022786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6064010	0.86[ASN][1000 genomes]
rs6064011	0.81[JPT][hapmap]
rs6068684	0.90[JPT][hapmap]
rs6068691	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs6091756	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6097632	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs6126982	0.89[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]

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
rs6097618	NFATC2	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52426200-52456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52443400-52456000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:52443800-52449000	Weak transcription	Lung	lung
4	chr20:52444000-52453200	Weak transcription	Small Intestine	intestine
5	chr20:52444800-52456000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:52446600-52455400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr20:52446800-52450200	Weak transcription	Fetal Muscle Leg	muscle
8	chr20:52446800-52450600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr20:52446800-52452000	Weak transcription	Thymus	Thymus
10	chr20:52447000-52449200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr20:52447000-52451600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr20:52447000-52452000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr20:52447000-52456000	Weak transcription	Placenta	Placenta
14	chr20:52447200-52449000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr20:52447200-52450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr20:52447200-52450600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr20:52447200-52450600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr20:52447200-52451400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr20:52447200-52451400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr20:52447200-52453400	Weak transcription	Fetal Intestine Small	intestine
21	chr20:52447200-52453400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr20:52447400-52449800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr20:52447400-52450000	Weak transcription	NHEK	skin
24	chr20:52447400-52450200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr20:52447400-52450200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr20:52447400-52450200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr20:52447400-52450200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr20:52447400-52450200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr20:52447400-52450400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr20:52447400-52450400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr20:52447400-52450400	Weak transcription	A549	lung
32	chr20:52447400-52450600	Weak transcription	Primary T cells from cord blood	blood
33	chr20:52447400-52450600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr20:52447400-52450600	Weak transcription	NH-A	brain
35	chr20:52447400-52450600	Weak transcription	Osteobl	bone
36	chr20:52447400-52452200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr20:52447400-52453600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr20:52447400-52456200	Weak transcription	HUVEC	blood vessel
39	chr20:52447400-52459400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr20:52447600-52450000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr20:52447600-52450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr20:52447600-52450200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr20:52447600-52450200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr20:52447600-52450200	Weak transcription	Dnd41	blood
45	chr20:52447600-52450400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr20:52447600-52450400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr20:52447600-52450600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr20:52447600-52450800	Weak transcription	HSMM	muscle
49	chr20:52447600-52453200	Weak transcription	Colonic Mucosa	Colon
50	chr20:52447800-52449200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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