Variant report

Variant	rs2038068
Chromosome Location	chr6:35374461-35374462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:35374379..35377300-chr6:35379343..35382186,2	K562	blood:
2	chr6:35368369..35371007-chr6:35374165..35376691,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1040436	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]
rs1053049	0.82[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1883322	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2016520	0.88[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2038067	0.97[CHD][hapmap];0.86[GIH][hapmap]
rs2076166	0.91[CHD][hapmap];0.80[GIH][hapmap]
rs2076167	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]
rs2076168	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2076169	0.86[CHD][hapmap]
rs2267665	0.91[CHD][hapmap];0.83[GIH][hapmap]
rs2267666	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267667	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267668	0.88[CHD][hapmap];0.83[GIH][hapmap]
rs2267669	0.90[CHD][hapmap];0.83[GIH][hapmap]
rs2395622	0.90[ASN][1000 genomes]
rs2395623	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3734254	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]
rs4713858	0.86[CHD][hapmap]
rs6457818	0.82[ASN][1000 genomes]
rs760783	0.88[CHD][hapmap];0.80[GIH][hapmap]
rs7749160	0.88[CHD][hapmap];0.80[GIH][hapmap]
rs7751481	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9462082	0.88[CHD][hapmap]
rs9462083	0.84[ASN][1000 genomes]
rs9462084	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2038068	TULP1	cis	cerebellum	SCAN

Chromatin state (count:93 , 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	chr6:35359800-35378800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:35360000-35378200	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:35360000-35378400	Weak transcription	HSMMtube	muscle
6	chr6:35360000-35379000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:35360000-35382600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:35360600-35378600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:35361000-35378000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:35361000-35378600	Weak transcription	Adipose Nuclei	Adipose
11	chr6:35361000-35378600	Weak transcription	NHLF	lung
12	chr6:35361000-35378800	Weak transcription	Psoas Muscle	Psoas
13	chr6:35361200-35376200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:35361200-35378600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:35361800-35385800	Weak transcription	Small Intestine	intestine
16	chr6:35362000-35378000	Weak transcription	Spleen	Spleen
17	chr6:35362200-35378400	Weak transcription	Primary B cells from cord blood	blood
18	chr6:35362200-35378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:35362200-35380000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:35363400-35378200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr6:35364000-35378000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr6:35365400-35375800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:35365400-35378600	Weak transcription	NHDF-Ad	bronchial
24	chr6:35365800-35377800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:35365800-35378600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:35365800-35378600	Weak transcription	Ovary	ovary
27	chr6:35366200-35378000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:35366200-35386800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:35366400-35382800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:35366600-35376600	Weak transcription	K562	blood
31	chr6:35366600-35378600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:35367800-35378600	Weak transcription	Thymus	Thymus
33	chr6:35369200-35378600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:35369200-35378800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:35369200-35379000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:35369200-35382600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:35369400-35382600	Weak transcription	NH-A	brain
38	chr6:35369600-35378000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:35369600-35378200	Weak transcription	Esophagus	oesophagus
40	chr6:35369800-35377600	Weak transcription	Osteobl	bone
41	chr6:35370200-35378200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr6:35370200-35378400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:35370600-35375800	Weak transcription	Fetal Muscle Leg	muscle
44	chr6:35370600-35375800	Weak transcription	HSMM	muscle
45	chr6:35370600-35378000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr6:35370600-35393200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:35370800-35378600	Weak transcription	Colonic Mucosa	Colon
48	chr6:35371000-35375600	Weak transcription	HMEC	breast
49	chr6:35371000-35376000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:35371000-35378000	Weak transcription	Rectal Mucosa Donor 31	rectum

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