Variant report

Variant	rs2076167
Chromosome Location	chr6:35391787-35391788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35369456..35371995-chr6:35391240..35394220,2	MCF-7	breast:
2	chr6:35385294..35388987-chr6:35389022..35393579,4	K562	blood:
3	chr6:35390370..35392093-chr6:35395033..35397221,2	K562	blood:
4	chr6:35389714..35392038-chr6:35454944..35457241,2	K562	blood:
5	chr6:35390023..35392138-chr6:35401114..35403193,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1040436	0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1053049	0.82[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883322	0.88[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2016520	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2038067	0.95[CHD][hapmap]
rs2038068	0.88[ASW][hapmap];0.86[CEU][hapmap];0.88[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2076166	0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs2076168	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2076169	0.88[CHD][hapmap]
rs2267665	0.88[CHD][hapmap]
rs2267666	0.95[CEU][hapmap];0.88[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2267667	0.95[CEU][hapmap];0.88[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2267668	0.91[CHD][hapmap]
rs2267669	0.93[CHD][hapmap]
rs2395622	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2395623	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3734254	1.00[ASW][hapmap];0.86[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713858	0.88[CHD][hapmap]
rs6457818	0.93[ASN][1000 genomes]
rs760783	0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs7749160	0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs7751481	0.95[CEU][hapmap];0.88[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9380508	0.85[ASN][1000 genomes]
rs9462082	0.91[CHD][hapmap]
rs9462083	0.95[ASN][1000 genomes]
rs9462084	0.95[ASN][1000 genomes]
rs9794	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv462907	chr6:35333799-35408959	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv602908	chr6:35333799-35408959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv602909	chr6:35356640-35423489	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv470812	chr6:35374461-35418118	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
7	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
8	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
9	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
10	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2076167	TULP1	cis	parietal	SCAN
rs2076167	SCUBE3	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35370600-35393200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:35377800-35395000	Weak transcription	K562	blood
3	chr6:35378800-35393400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:35379800-35392600	Strong transcription	NHEK	skin
5	chr6:35380400-35392200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:35380400-35392200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:35383000-35394600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:35383000-35396800	Weak transcription	Right Atrium	heart
9	chr6:35383400-35394800	Weak transcription	Fetal Kidney	kidney
10	chr6:35383400-35396600	Weak transcription	Stomach Mucosa	stomach
11	chr6:35383600-35392000	Weak transcription	Brain Germinal Matrix	brain
12	chr6:35383600-35402600	Weak transcription	Fetal Heart	heart
13	chr6:35384200-35392800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:35385600-35392400	Strong transcription	Esophagus	oesophagus
15	chr6:35387400-35393200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:35387400-35393400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:35387400-35395200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:35387600-35391800	Strong transcription	Spleen	Spleen
19	chr6:35387600-35392600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:35387600-35394000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:35387600-35394800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:35387600-35395200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:35387600-35395200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr6:35387800-35392000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:35387800-35392400	Weak transcription	NH-A	brain
26	chr6:35387800-35392600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr6:35387800-35392800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:35387800-35393200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:35387800-35393200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:35387800-35393400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr6:35387800-35394600	Strong transcription	Fetal Stomach	stomach
32	chr6:35387800-35396000	Strong transcription	Fetal Intestine Small	intestine
33	chr6:35388000-35391800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:35388000-35392000	Strong transcription	Placenta	Placenta
35	chr6:35388000-35392000	Strong transcription	Lung	lung
36	chr6:35388000-35392600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr6:35388000-35393400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:35388000-35393400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr6:35388000-35394200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:35388000-35395600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr6:35388000-35396000	Strong transcription	Fetal Muscle Leg	muscle
42	chr6:35388200-35392200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:35388200-35393600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:35388200-35395200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:35388400-35392000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:35388400-35393200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr6:35388400-35393200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:35389200-35393200	Strong transcription	Adipose Nuclei	Adipose
49	chr6:35389200-35393400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr6:35389200-35395200	Strong transcription	Duodenum Mucosa	Duodenum

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