Variant report

Variant	rs2472797
Chromosome Location	chr6:14763148-14763149
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:14762299..14764656-chr6:15088901..15090764,2	MCF-7	breast:
2	chr6:14762038..14763627-chr6:14854047..14856910,2	MCF-7	breast:
3	chr6:14761235..14763388-chr6:14768034..14770396,2	K562	blood:
4	chr6:14762306..14764528-chr6:14766807..14769231,2	K562	blood:
5	chr6:14761733..14764383-chr6:14771146..14773076,2	K562	blood:
6	chr6:14743112..14746025-chr6:14761526..14763688,5	MCF-7	breast:
7	chr6:14762315..14764883-chr6:15247297..15249027,2	MCF-7	breast:
8	chr6:14756302..14759607-chr6:14761530..14763562,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000234261	Chromatin interaction
ENSG00000235488	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1010703	1.00[JPT][hapmap]
rs1010704	1.00[JPT][hapmap]
rs2038017	0.92[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs2472789	1.00[JPT][hapmap]
rs2472790	1.00[JPT][hapmap]
rs2472791	1.00[JPT][hapmap]
rs2472793	1.00[ASN][1000 genomes]
rs2472798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2472802	0.93[MEX][hapmap]
rs2500066	1.00[JPT][hapmap]
rs2500067	1.00[JPT][hapmap]
rs2500071	1.00[JPT][hapmap]
rs2500076	1.00[JPT][hapmap]
rs2500077	1.00[JPT][hapmap]
rs2500078	1.00[ASN][1000 genomes]
rs2500079	1.00[ASN][1000 genomes]
rs4145445	1.00[JPT][hapmap]
rs4145447	1.00[JPT][hapmap]
rs4145448	1.00[JPT][hapmap]
rs4715922	1.00[JPT][hapmap]
rs6459373	1.00[JPT][hapmap]
rs6459374	1.00[JPT][hapmap]
rs6459375	1.00[JPT][hapmap]
rs6919669	1.00[JPT][hapmap]
rs6935110	1.00[JPT][hapmap]
rs7743941	1.00[ASN][1000 genomes]
rs7744561	1.00[JPT][hapmap]
rs7766310	1.00[JPT][hapmap]
rs926242	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9396530	1.00[JPT][hapmap]
rs9396531	1.00[JPT][hapmap]
rs9476648	0.90[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462641	chr6:14203872-14764983	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv600997	chr6:14203872-14764983	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1023685	chr6:14514647-14838390	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2472797	CAP2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:14743600-14767400	Weak transcription	Right Atrium	heart
2	chr6:14758200-14764200	Enhancers	Liver	Liver
3	chr6:14758400-14764600	Enhancers	Fetal Intestine Large	intestine
4	chr6:14758800-14766800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:14759000-14763400	Weak transcription	Stomach Mucosa	stomach
6	chr6:14759200-14763200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:14759200-14763200	Weak transcription	Hela-S3	cervix
8	chr6:14759200-14764400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:14759200-14767800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:14759600-14764400	Enhancers	Fetal Intestine Small	intestine
11	chr6:14760400-14772400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:14760800-14765400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr6:14761000-14765200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr6:14761000-14766000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:14762000-14763600	Enhancers	K562	blood
16	chr6:14762000-14764200	Enhancers	HepG2	liver
17	chr6:14762200-14764200	Enhancers	Small Intestine	intestine
18	chr6:14762400-14764200	Enhancers	Duodenum Mucosa	Duodenum
19	chr6:14762600-14763400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:14762600-14764200	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr6:14762600-14766000	Enhancers	Placenta	Placenta
22	chr6:14762800-14763400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:14762800-14763400	Enhancers	A549	lung
24	chr6:14762800-14763600	Enhancers	Left Ventricle	heart
25	chr6:14762800-14763600	Enhancers	NHEK	skin
26	chr6:14762800-14764000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:14762800-14764000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:14762800-14764200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:14762800-14764200	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr6:14762800-14765400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:14762800-14765600	Enhancers	HMEC	breast
32	chr6:14763000-14764000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:14763000-14764000	Enhancers	NHLF	lung
34	chr6:14763000-14770400	Weak transcription	Adipose Nuclei	Adipose

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