Variant report

Variant	rs1040436
Chromosome Location	chr6:35367909-35367910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1053049	0.87[ASW][hapmap];0.87[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1883322	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2016520	0.88[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2038067	0.95[CHD][hapmap];0.80[GIH][hapmap]
rs2038068	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076166	0.88[CHD][hapmap]
rs2076167	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]
rs2076168	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2076169	0.88[CHD][hapmap]
rs2267665	0.88[CHD][hapmap]
rs2267666	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267667	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267668	0.86[CHD][hapmap]
rs2267669	0.88[CHD][hapmap]
rs2395622	0.87[ASN][1000 genomes]
rs2395623	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3734254	0.82[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4713858	0.88[CHD][hapmap]
rs760783	0.91[CHD][hapmap]
rs7749160	0.91[CHD][hapmap]
rs7751481	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9462082	0.86[CHD][hapmap]
rs9462083	0.81[ASN][1000 genomes]
rs9462084	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1040436	TULP1	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35338400-35378400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:35345600-35378400	Weak transcription	Aorta	Aorta
3	chr6:35354000-35372400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:35359600-35369200	Weak transcription	Fetal Kidney	kidney
5	chr6:35359800-35378800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:35360000-35378200	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:35360000-35378400	Weak transcription	HSMMtube	muscle
8	chr6:35360000-35379000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:35360000-35382600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:35360400-35372000	Weak transcription	Brain Angular Gyrus	brain
11	chr6:35360400-35372200	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:35360600-35372400	Weak transcription	Brain Anterior Caudate	brain
13	chr6:35360600-35378600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:35361000-35378000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:35361000-35378600	Weak transcription	Adipose Nuclei	Adipose
16	chr6:35361000-35378600	Weak transcription	NHLF	lung
17	chr6:35361000-35378800	Weak transcription	Psoas Muscle	Psoas
18	chr6:35361200-35376200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:35361200-35378600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:35361800-35385800	Weak transcription	Small Intestine	intestine
21	chr6:35362000-35368800	Weak transcription	Right Ventricle	heart
22	chr6:35362000-35378000	Weak transcription	Spleen	Spleen
23	chr6:35362200-35368600	Weak transcription	Lung	lung
24	chr6:35362200-35378400	Weak transcription	Primary B cells from cord blood	blood
25	chr6:35362200-35378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr6:35362200-35380000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:35362600-35368800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:35362800-35368000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:35362800-35370200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:35363000-35369200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:35363400-35378200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:35363600-35369000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:35363800-35368000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:35363800-35371600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:35364000-35378000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr6:35365000-35368600	Weak transcription	HSMM	muscle
37	chr6:35365200-35368000	Weak transcription	Pancreas	Pancrea
38	chr6:35365200-35368200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr6:35365200-35368600	Weak transcription	HepG2	liver
40	chr6:35365400-35368200	Weak transcription	Stomach Mucosa	stomach
41	chr6:35365400-35368600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:35365400-35368600	Weak transcription	NH-A	brain
43	chr6:35365400-35368800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:35365400-35368800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:35365400-35375800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:35365400-35378600	Weak transcription	NHDF-Ad	bronchial
47	chr6:35365600-35368200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:35365600-35370200	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:35365800-35368200	Weak transcription	Placenta	Placenta
50	chr6:35365800-35368600	Weak transcription	Left Ventricle	heart

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