Variant report

Variant	rs7652801
Chromosome Location	chr3:113008606-113008607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113006518..113009252-chr3:113022615..113024220,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206530	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10511324	0.81[EUR][1000 genomes]
rs13326562	0.81[EUR][1000 genomes]
rs16860734	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28679287	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3995908	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6438134	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6763234	1.00[CEU][hapmap]
rs6780720	1.00[CEU][hapmap]
rs6808103	1.00[CEU][hapmap]
rs7625829	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs7629636	1.00[CEU][hapmap]
rs9288980	0.81[EUR][1000 genomes]
rs9810059	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs9811168	0.81[EUR][1000 genomes]
rs9819129	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9820627	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9823770	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9831049	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9831364	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9831793	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9832953	0.82[YRI][hapmap]
rs9836199	0.81[EUR][1000 genomes]
rs9837357	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9840485	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9851183	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[EUR][1000 genomes]
rs9852068	1.00[CEU][hapmap]
rs9853439	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9863114	0.81[EUR][1000 genomes]
rs9864630	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9869371	1.00[AMR][1000 genomes];0.86[EUR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv521829	chr3:113007525-113010950	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7652801	CCL3	trans	brain	seeQTL
rs7652801	KLF4	trans	brain	seeQTL
rs7652801	TNFRSF11B	trans	brain	seeQTL
rs7652801	CCL3L1	trans	brain	seeQTL
rs7652801	PRG4	trans	brain	seeQTL
rs7652801	SIK1	trans	brain	seeQTL
rs7652801	DUSP1	trans	brain	seeQTL
rs7652801	BTG2	trans	brain	seeQTL
rs7652801	PHLDB2	trans	brain	seeQTL
rs7652801	OMD	trans	brain	seeQTL
rs7652801	FAT4	trans	brain	seeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
4	chr3:112995200-113016000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:112995200-113022400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:112995400-113024000	Weak transcription	Aorta	Aorta
7	chr3:112995400-113035800	Weak transcription	Lung	lung
8	chr3:112995800-113013000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:112995800-113035800	Weak transcription	Thymus	Thymus
10	chr3:112996000-113025400	Weak transcription	Small Intestine	intestine
11	chr3:112996200-113034400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:112996400-113046400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:112997200-113036200	Weak transcription	Spleen	Spleen
14	chr3:112998600-113036000	Weak transcription	Gastric	stomach
15	chr3:113000200-113016400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:113000800-113014400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:113001200-113025400	Weak transcription	Brain Anterior Caudate	brain
18	chr3:113001200-113044600	Weak transcription	Fetal Kidney	kidney
19	chr3:113003200-113015400	Weak transcription	Brain Germinal Matrix	brain
20	chr3:113003400-113022600	Weak transcription	Colonic Mucosa	Colon
21	chr3:113003800-113016200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:113003800-113023000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:113004200-113023800	Weak transcription	Brain Substantia Nigra	brain
24	chr3:113004600-113016200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:113005600-113029800	Weak transcription	Fetal Intestine Large	intestine
26	chr3:113006200-113009000	Weak transcription	Fetal Lung	lung
27	chr3:113006200-113009400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:113006200-113010400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:113006200-113010400	Weak transcription	Ovary	ovary
30	chr3:113006200-113035400	Weak transcription	Esophagus	oesophagus
31	chr3:113006200-113036000	Weak transcription	Pancreas	Pancrea
32	chr3:113006400-113009000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:113006400-113009600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:113006600-113024000	Weak transcription	HSMMtube	muscle
35	chr3:113006800-113010800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:113006800-113015800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:113006800-113022600	Weak transcription	Hela-S3	cervix
38	chr3:113006800-113031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:113007000-113010200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:113007000-113010600	Weak transcription	NHDF-Ad	bronchial
41	chr3:113007000-113012400	Weak transcription	A549	lung
42	chr3:113007000-113016400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:113007000-113022000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:113007000-113022600	Weak transcription	Liver	Liver
45	chr3:113007000-113022800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:113007000-113023800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:113007000-113028000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:113007000-113034400	Weak transcription	HSMM	muscle
49	chr3:113007200-113043400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:113007600-113008800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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