Variant report

Variant	rs8541
Chromosome Location	chr6:13290238-13290239
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	chr6:13287477..13291631-chr6:13573758..13576939,3	K562	blood:
2	chr6:13290208..13292111-chr6:13295404..13298068,2	K562	blood:

Variant related genes	Relation type
ENSG00000124523	Chromatin interaction
ENSG00000215022	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11759028	0.83[ASN][1000 genomes]
rs1223393	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs12697949	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs1550526	1.00[CEU][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs182148	0.90[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2002961	0.80[GIH][hapmap]
rs202028	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs202030	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202034	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs202038	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202040	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202042	0.83[CEU][hapmap]
rs202044	0.83[CEU][hapmap]
rs202045	0.81[CEU][hapmap]
rs202048	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs202053	0.83[CEU][hapmap]
rs202064	0.81[CEU][hapmap];0.90[MEX][hapmap]
rs202068	0.81[EUR][1000 genomes]
rs202069	0.90[CEU][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs202070	0.83[CEU][hapmap]
rs202071	0.83[CEU][hapmap]
rs202072	0.83[CEU][hapmap]
rs202073	0.83[CEU][hapmap]
rs35952102	0.85[ASN][1000 genomes]
rs377704	0.83[CEU][hapmap]
rs3800481	0.88[GIH][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs3800482	0.94[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs3800483	0.85[ASN][1000 genomes]
rs3800484	0.85[ASN][1000 genomes]
rs3800485	0.94[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs3800486	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3823442	0.81[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3823443	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs405078	0.83[CEU][hapmap]
rs413120	0.83[CEU][hapmap]
rs441213	0.83[CEU][hapmap]
rs445714	0.83[CEU][hapmap]
rs453695	0.81[CEU][hapmap];0.90[MEX][hapmap]
rs454563	1.00[CEU][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4602719	1.00[CEU][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs515111	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6914796	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7742398	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9296641	0.80[GIH][hapmap]
rs9296642	0.80[GIH][hapmap]
rs9473908	0.82[JPT][hapmap]
rs9473929	0.81[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9473930	0.81[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.85[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8541	TBC1D7	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13270200-13291600	Weak transcription	HSMM	muscle
2	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
3	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
4	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:13280000-13292600	Weak transcription	NHLF	lung
7	chr6:13280200-13292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:13282800-13291600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:13284000-13293000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:13284000-13294200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
12	chr6:13285800-13293000	Weak transcription	Brain Angular Gyrus	brain
13	chr6:13285800-13293000	Weak transcription	Brain Substantia Nigra	brain
14	chr6:13286600-13291600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:13286600-13292800	Weak transcription	Colonic Mucosa	Colon
16	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:13287200-13292000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:13287200-13292800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:13287400-13294400	Weak transcription	Fetal Kidney	kidney
20	chr6:13287800-13291800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:13287800-13294200	Weak transcription	A549	lung
22	chr6:13287800-13295200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr6:13287800-13298200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:13288000-13290600	Strong transcription	Left Ventricle	heart
25	chr6:13288000-13292200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr6:13288000-13294600	Weak transcription	Fetal Brain Male	brain
27	chr6:13288000-13296200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr6:13288200-13290400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:13288200-13291600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:13288200-13291600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:13288200-13291600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:13288200-13291600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:13288200-13291600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:13288200-13291600	Weak transcription	Brain Germinal Matrix	brain
35	chr6:13288200-13291600	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:13288200-13291600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:13288200-13292600	Weak transcription	Placenta	Placenta
38	chr6:13288200-13294200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:13288200-13294200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:13288200-13295400	Weak transcription	Fetal Heart	heart
41	chr6:13288200-13296400	Strong transcription	GM12878-XiMat	blood
42	chr6:13288400-13290400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr6:13288400-13290600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr6:13288400-13291600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:13288400-13293200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr6:13288400-13294200	Weak transcription	Osteobl	bone
47	chr6:13288400-13294800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:13288400-13302600	Weak transcription	Hela-S3	cervix
49	chr6:13288400-13302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr6:13288600-13290600	Strong transcription	Fetal Muscle Trunk	muscle

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