Variant report

Variant	rs1718235
Chromosome Location	chr3:99583484-99583485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99582999..99585506-chr3:99592416..99595464,3	MCF-7	breast:
2	chr3:99574024..99577676-chr3:99581622..99586745,5	K562	blood:
3	chr3:99575233..99577676-chr3:99581601..99584216,3	K562	blood:
4	chr3:99582314..99585905-chr3:99590964..99594499,4	MCF-7	breast:
5	chr3:99582343..99586390-chr3:99587207..99589734,4	MCF-7	breast:
6	chr3:99583225..99585048-chr3:99585235..99587325,2	K562	blood:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10936003	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1287284	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs13059754	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap]
rs1384062	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1610509	0.86[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs16841874	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1711564	0.82[LWK][hapmap];0.85[YRI][hapmap]
rs4577503	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs4928150	0.84[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4928151	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs4928230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928237	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs58704213	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440967	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs669676	0.83[ASW][hapmap];0.82[LWK][hapmap];0.85[YRI][hapmap]
rs6788750	0.84[LWK][hapmap];0.94[MKK][hapmap]
rs6802817	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs6806323	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs704571	0.94[JPT][hapmap]
rs704572	1.00[JPT][hapmap];0.90[YRI][hapmap]
rs704574	0.86[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs7613864	0.85[ASN][1000 genomes]
rs7649349	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs7650727	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs766778	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs792831	0.94[JPT][hapmap]
rs792833	0.86[CHD][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs792835	0.86[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs792836	0.94[JPT][hapmap]
rs792837	0.94[JPT][hapmap]
rs793437	0.83[ASN][1000 genomes]
rs793439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793443	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793446	0.84[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs793450	0.95[LWK][hapmap];0.88[MKK][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs793456	0.82[ASN][1000 genomes]
rs793464	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs793469	0.95[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes]
rs793475	0.84[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs793476	0.87[ASN][1000 genomes]
rs793482	0.86[LWK][hapmap];0.92[YRI][hapmap]
rs793483	0.82[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs793485	0.94[JPT][hapmap]
rs793497	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs793502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796976	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs813218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902159	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs923472	0.84[CEU][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1718235	SENP7	cis	parietal	SCAN
rs1718235	C3orf26	cis	multi-tissue	Pritchard
rs1718235	OR5H6	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:99565200-99585000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:99565600-99584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:99565600-99589400	Weak transcription	K562	blood
7	chr3:99569000-99589600	Weak transcription	Colonic Mucosa	Colon
8	chr3:99573200-99594000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:99573400-99589200	Genic enhancers	HepG2	liver
10	chr3:99573600-99584800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:99574000-99584000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:99574400-99590000	Weak transcription	Liver	Liver
13	chr3:99575000-99587000	Weak transcription	Pancreas	Pancrea
14	chr3:99575000-99593600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:99575200-99587000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:99576000-99587600	Genic enhancers	NHDF-Ad	bronchial
17	chr3:99576400-99585000	Weak transcription	A549	lung
18	chr3:99577400-99587200	Weak transcription	Brain Anterior Caudate	brain
19	chr3:99578200-99585400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:99578800-99584400	Strong transcription	Fetal Intestine Large	intestine
21	chr3:99579200-99591000	Genic enhancers	NH-A	brain
22	chr3:99579400-99587000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:99579400-99591000	Weak transcription	Fetal Lung	lung
24	chr3:99579600-99584000	Weak transcription	HMEC	breast
25	chr3:99579600-99585200	Weak transcription	Small Intestine	intestine
26	chr3:99579600-99585400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:99579600-99592400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:99580400-99585200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:99580400-99585200	Weak transcription	Fetal Kidney	kidney
30	chr3:99580400-99585400	Strong transcription	Fetal Muscle Leg	muscle
31	chr3:99580600-99585200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:99580600-99587000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:99580600-99587600	Weak transcription	Brain Angular Gyrus	brain
34	chr3:99580800-99590800	Weak transcription	Lung	lung
35	chr3:99581200-99589200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:99581400-99583600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:99581400-99585400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:99581400-99585400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:99581400-99594000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:99581600-99583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:99581600-99585000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:99581800-99589600	Weak transcription	Gastric	stomach
43	chr3:99582000-99583600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:99582000-99583600	Strong transcription	Primary B cells from cord blood	blood
45	chr3:99582000-99584200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:99582000-99587200	Weak transcription	Spleen	Spleen
47	chr3:99582000-99589400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:99582000-99589400	Weak transcription	Right Ventricle	heart
49	chr3:99582200-99584000	Strong transcription	HSMM	muscle
50	chr3:99582200-99584400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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