Variant report

Variant	rs7653015
Chromosome Location	chr3:42869216-42869217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42863918..42866711-chr3:42866825..42870903,9	MCF-7	breast:
2	chr3:42866999..42869697-chr3:42869826..42873026,3	K562	blood:
3	chr3:42866915..42869697-chr3:42869826..42874147,5	K562	blood:
4	chr3:42854558..42863000-chr3:42863307..42874321,18	MCF-7	breast:
5	chr3:42823380..42825503-chr3:42869037..42871310,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144648	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11716959	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17074834	0.81[JPT][hapmap]
rs3732861	0.91[JPT][hapmap]
rs6782601	0.94[CEU][hapmap];0.84[GIH][hapmap]
rs735320	0.94[CEU][hapmap]

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	esv1847016	chr3:42855765-42880490	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7653015	RTP3	cis	cerebellum	SCAN
rs7653015	KIF15	cis	parietal	SCAN
rs7653015	HIGD1A	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42857000-42869800	Weak transcription	Colonic Mucosa	Colon
2	chr3:42861600-42873000	Weak transcription	Esophagus	oesophagus
3	chr3:42861600-42885400	Weak transcription	Pancreas	Pancrea
4	chr3:42861800-42872600	Weak transcription	Brain Anterior Caudate	brain
5	chr3:42862400-42872800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:42863000-42870200	Weak transcription	Hela-S3	cervix
7	chr3:42863000-42871000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:42865200-42870400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:42865400-42870600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:42865400-42871000	Weak transcription	Adipose Nuclei	Adipose
11	chr3:42865400-42872200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:42867200-42869400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:42867200-42870400	Enhancers	HepG2	liver
14	chr3:42868400-42869400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:42868400-42874200	Enhancers	Liver	Liver
16	chr3:42868600-42869400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:42868600-42869400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:42868600-42869400	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr3:42868600-42873200	Enhancers	HMEC	breast
20	chr3:42868800-42869400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr3:42869000-42869400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:42869000-42869400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr3:42869000-42869400	Enhancers	NHEK	skin
24	chr3:42869000-42870600	Enhancers	Fetal Intestine Large	intestine
25	chr3:42869000-42870800	Enhancers	Fetal Intestine Small	intestine
26	chr3:42869000-42871200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr3:42869000-42872400	Enhancers	Stomach Mucosa	stomach
28	chr3:42869200-42869400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:42869200-42869400	Enhancers	Placenta	Placenta
30	chr3:42869200-42869400	Enhancers	K562	blood
31	chr3:42869200-42870200	Enhancers	Small Intestine	intestine
32	chr3:42869200-42870600	Enhancers	Duodenum Mucosa	Duodenum

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