Variant report

Variant	rs6787229
Chromosome Location	chr3:46889187-46889188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46888247..46890216-chr3:46894396..46896152,2	MCF-7	breast:
2	chr3:46888493..46890387-chr3:46908192..46909889,2	K562	blood:
3	chr3:46888374..46889993-chr3:46908092..46909889,2	K562	blood:
4	chr3:46732249..46733917-chr3:46887547..46889689,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1077216	0.96[ASN][1000 genomes]
rs2242118	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3729704	0.90[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3792557	0.90[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs56387622	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61351097	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs66668401	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs67529903	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768627	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6768845	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6778660	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6781266	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6786689	0.99[ASN][1000 genomes]
rs6793661	0.80[CHB][hapmap]
rs6796502	0.90[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs6808303	0.80[CHB][hapmap]
rs72895203	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73065118	0.81[ASN][1000 genomes]
rs73065135	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73065147	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv590204	chr3:46852679-46901654	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv590205	chr3:46852679-46929546	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv590206	chr3:46873957-46935527	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6787229	SCAP	cis	parietal	SCAN
rs6787229	CYP8B1	cis	cerebellum	SCAN
rs6787229	PRSS46	cis	Thyroid	GTEx
rs6787229	TRAIP	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46887200-46889200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:46887200-46890800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:46887400-46890200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:46887800-46889400	Enhancers	Left Ventricle	heart
5	chr3:46888000-46889800	Weak transcription	HSMM	muscle
6	chr3:46888000-46890000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:46888000-46891600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:46888000-46892200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:46888000-46908800	Weak transcription	Esophagus	oesophagus
10	chr3:46888200-46889200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:46888200-46889200	Enhancers	Right Atrium	heart
12	chr3:46888200-46889800	Weak transcription	Fetal Lung	lung
13	chr3:46888200-46889800	Weak transcription	Ovary	ovary
14	chr3:46888200-46890000	Weak transcription	HSMMtube	muscle
15	chr3:46888200-46892200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:46888400-46889200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr3:46888400-46889600	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:46888400-46889800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:46888400-46889800	Weak transcription	Fetal Kidney	kidney
20	chr3:46888400-46890000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:46888400-46890000	Weak transcription	Liver	Liver
22	chr3:46888400-46890000	Weak transcription	HUVEC	blood vessel
23	chr3:46888400-46890000	Enhancers	NHDF-Ad	bronchial
24	chr3:46888400-46890200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:46888400-46890600	Weak transcription	Brain Germinal Matrix	brain
26	chr3:46888400-46891600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:46888400-46892000	Enhancers	Fetal Intestine Large	intestine
28	chr3:46888400-46892200	Enhancers	Right Ventricle	heart
29	chr3:46888600-46889200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:46888600-46889800	Weak transcription	Lung	lung
31	chr3:46888600-46889800	Weak transcription	Spleen	Spleen
32	chr3:46888600-46890000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:46888600-46890000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:46888600-46891400	Enhancers	Adipose Nuclei	Adipose
35	chr3:46888600-46891800	Enhancers	Fetal Intestine Small	intestine
36	chr3:46888800-46889200	Flanking Active TSS	Fetal Heart	heart
37	chr3:46888800-46890200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
38	chr3:46888800-46891600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr3:46888800-46892200	Enhancers	Fetal Muscle Trunk	muscle
40	chr3:46889000-46889200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
41	chr3:46889000-46889600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:46889000-46890000	Weak transcription	Pancreas	Pancrea
43	chr3:46889000-46891800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:46889000-46892000	Enhancers	Fetal Muscle Leg	muscle

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