Variant report

Variant	rs7756267
Chromosome Location	chr6:38359599-38359600
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	chr6:38354681..38357070-chr6:38359455..38361170,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1983605	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2294739	0.89[EUR][1000 genomes]
rs4140443	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4711538	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4711540	0.86[EUR][1000 genomes]
rs4711541	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4711543	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4711544	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4711546	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4714151	0.88[EUR][1000 genomes]
rs4714152	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4714153	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4714155	1.00[CEU][hapmap];0.87[YRI][hapmap];0.99[EUR][1000 genomes]
rs4714156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4714157	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4714158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58424668	0.87[EUR][1000 genomes]
rs58807047	0.87[EUR][1000 genomes]
rs6903060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6903611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6903767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6923701	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs742515	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7743023	0.99[EUR][1000 genomes]
rs7748599	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7749685	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7759078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7759629	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7764502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7766214	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9296248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296249	1.00[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs9349076	0.96[EUR][1000 genomes]
rs9349077	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs9349078	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9349079	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9357269	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357270	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357272	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9366957	0.84[EUR][1000 genomes]
rs9366959	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9366960	0.98[EUR][1000 genomes]
rs9369055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9369057	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs9380740	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9380741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9380742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380743	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9380745	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs9380747	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394493	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9394494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9470865	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9470867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470874	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv602957	chr6:38305770-38395874	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv966638	chr6:38353527-38361086	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7756267	TDRG1	cis	cerebellum	SCAN
rs7756267	PACSIN1	cis	cerebellum	SCAN
rs7756267	KCNK5	cis	cerebellum	SCAN
rs7756267	GLO1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38343000-38367800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:38350200-38366200	Weak transcription	Lung	lung
3	chr6:38354000-38376000	Weak transcription	Primary T cells from cord blood	blood
4	chr6:38354800-38370800	Weak transcription	Primary B cells from cord blood	blood
5	chr6:38356400-38359600	Weak transcription	Adipose Nuclei	Adipose
6	chr6:38356600-38359600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:38358400-38359800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr6:38358400-38360400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr6:38358400-38361200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr6:38358600-38360200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:38358600-38360400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:38358600-38360800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr6:38358800-38359800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:38358800-38360000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:38358800-38360000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr6:38358800-38360000	Enhancers	Hela-S3	cervix
17	chr6:38358800-38360200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:38358800-38360400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr6:38358800-38360400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr6:38358800-38360400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:38358800-38360400	Enhancers	NHDF-Ad	bronchial
22	chr6:38358800-38360400	Enhancers	NHLF	lung
23	chr6:38358800-38361200	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr6:38358800-38362200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:38358800-38362800	Enhancers	HUVEC	blood vessel
26	chr6:38359000-38359600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:38359000-38359800	Enhancers	Fetal Heart	heart
28	chr6:38359000-38360000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:38359000-38360000	Enhancers	A549	lung
30	chr6:38359000-38360200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr6:38359000-38360200	Enhancers	HSMMtube	muscle
32	chr6:38359000-38360200	Enhancers	NH-A	brain
33	chr6:38359000-38360400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:38359200-38360000	Enhancers	NHEK	skin
35	chr6:38359400-38359600	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr6:38359400-38359800	Enhancers	Osteobl	bone
37	chr6:38359400-38360000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:38359400-38360000	Enhancers	Psoas Muscle	Psoas
39	chr6:38359400-38360000	Enhancers	HepG2	liver
40	chr6:38359400-38360400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:38359400-38360400	Enhancers	Brain Germinal Matrix	brain
42	chr6:38359400-38360600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:38359400-38360600	Enhancers	Cortex derived primary cultured neurospheres	brain

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