Variant report

Variant	rs3734254
Chromosome Location	chr6:35395010-35395011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35226026..35228002-chr6:35394504..35397292,2	K562	blood:
2	chr6:35380537..35383478-chr6:35394277..35398227,3	K562	blood:
3	chr6:35388873..35391570-chr6:35394373..35396733,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065029	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1040436	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]
rs1053049	0.82[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883322	0.88[ASW][hapmap];0.82[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2016520	0.93[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2038067	0.90[CHD][hapmap]
rs2038068	0.88[ASW][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2076166	0.88[CHD][hapmap];0.80[GIH][hapmap];0.84[ASN][1000 genomes]
rs2076167	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]
rs2076168	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2076169	0.88[CHD][hapmap]
rs2267665	0.83[CHD][hapmap]
rs2267666	0.82[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2267667	0.82[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2267668	0.85[CHD][hapmap]
rs2267669	0.88[CHD][hapmap]
rs2395622	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2395623	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713858	0.90[CHD][hapmap]
rs6457818	0.94[ASN][1000 genomes]
rs760783	0.90[CHD][hapmap];0.80[GIH][hapmap];0.84[ASN][1000 genomes]
rs7749160	0.90[CHD][hapmap];0.80[GIH][hapmap];0.83[ASN][1000 genomes]
rs7751481	0.82[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9380508	0.86[ASN][1000 genomes]
rs9462082	0.85[CHD][hapmap]
rs9462083	0.96[ASN][1000 genomes]
rs9462084	0.96[ASN][1000 genomes]
rs9794	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
11	nsv885800	chr6:35394247-35406153	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3734254	TULP1	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35383000-35396800	Weak transcription	Right Atrium	heart
2	chr6:35383400-35396600	Weak transcription	Stomach Mucosa	stomach
3	chr6:35383600-35402600	Weak transcription	Fetal Heart	heart
4	chr6:35387400-35395200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:35387600-35395200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:35387600-35395200	Strong transcription	Stomach Smooth Muscle	stomach
7	chr6:35387800-35396000	Strong transcription	Fetal Intestine Small	intestine
8	chr6:35388000-35395600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr6:35388000-35396000	Strong transcription	Fetal Muscle Leg	muscle
10	chr6:35388200-35395200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:35389200-35395200	Strong transcription	Duodenum Mucosa	Duodenum
12	chr6:35389200-35395400	Strong transcription	Fetal Intestine Large	intestine
13	chr6:35389200-35396000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:35389400-35395200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:35389400-35395200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:35389400-35395600	Strong transcription	Primary T cells from cord blood	blood
17	chr6:35389400-35395600	Strong transcription	Brain Cingulate Gyrus	brain
18	chr6:35389400-35395600	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:35389400-35395800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:35389600-35395200	Strong transcription	Left Ventricle	heart
21	chr6:35389600-35395400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:35389600-35395600	Strong transcription	Brain Anterior Caudate	brain
23	chr6:35389600-35395600	Strong transcription	Brain Hippocampus Middle	brain
24	chr6:35389600-35396200	Strong transcription	Gastric	stomach
25	chr6:35390400-35395200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:35390400-35396000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:35391400-35395600	Strong transcription	Colonic Mucosa	Colon
28	chr6:35391400-35396000	Strong transcription	Thymus	Thymus
29	chr6:35391400-35396400	Strong transcription	Right Ventricle	heart
30	chr6:35391600-35395200	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr6:35391600-35395600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:35391800-35395600	Strong transcription	Psoas Muscle	Psoas
33	chr6:35391800-35395800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:35391800-35396200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:35392000-35395800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:35392400-35396600	Weak transcription	Small Intestine	intestine
37	chr6:35392400-35397200	Genic enhancers	NHLF	lung
38	chr6:35392600-35395800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:35392600-35396000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr6:35392600-35396200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr6:35392600-35396200	Enhancers	HUVEC	blood vessel
42	chr6:35392600-35402800	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:35392800-35396000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:35393200-35396400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr6:35393200-35396400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:35393200-35397200	Enhancers	H1 Cell Line	embryonic stem cell
47	chr6:35393400-35397000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:35393600-35395200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:35393600-35395200	Strong transcription	Ovary	ovary
50	chr6:35393600-35396000	Enhancers	NH-A	brain

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