Variant report

Variant	rs6460339
Chromosome Location	chr7:66786212-66786213
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10085684	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10227991	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10242530	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10278852	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10280504	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11975662	0.92[ASN][1000 genomes]
rs12673116	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12698580	0.89[EUR][1000 genomes]
rs13438181	0.85[EUR][1000 genomes]
rs2075082	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28540856	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28542443	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28718590	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4521652	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6945404	0.89[EUR][1000 genomes]
rs6957404	0.87[ASN][1000 genomes]
rs6957846	0.87[ASN][1000 genomes]
rs73135830	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73148449	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs73148464	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73148486	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73150465	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73150492	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73150498	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73152206	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7779003	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7789199	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9654869	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1027702	chr7:66722103-66841913	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv1031048	chr7:66722103-66844039	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv970873	chr7:66785229-66793852	Weak transcription Strong transcription Enhancers Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66770400-66786800	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr7:66770600-66786400	Weak transcription	Fetal Heart	heart
3	chr7:66770800-66786800	Strong transcription	Liver	Liver
4	chr7:66775200-66807600	Weak transcription	Colonic Mucosa	Colon
5	chr7:66775800-66786400	Weak transcription	NHLF	lung
6	chr7:66777200-66789400	Weak transcription	NHDF-Ad	bronchial
7	chr7:66777200-66805200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr7:66777400-66787000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:66777600-66786600	Weak transcription	HMEC	breast
10	chr7:66778400-66787200	Weak transcription	Pancreas	Pancrea
11	chr7:66778800-66809000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:66779000-66787200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:66779600-66786600	Weak transcription	HSMM	muscle
14	chr7:66779800-66807600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr7:66780000-66786800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:66780200-66786800	Weak transcription	Osteobl	bone
17	chr7:66780200-66788800	Weak transcription	Aorta	Aorta
18	chr7:66780400-66787000	Weak transcription	K562	blood
19	chr7:66780400-66788200	Weak transcription	NHEK	skin
20	chr7:66780400-66790800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:66780400-66791000	Weak transcription	Primary B cells from cord blood	blood
22	chr7:66780400-66791800	Weak transcription	Fetal Lung	lung
23	chr7:66780400-66804600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr7:66780400-66808200	Weak transcription	GM12878-XiMat	blood
25	chr7:66780400-66809400	Weak transcription	A549	lung
26	chr7:66781200-66804600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr7:66781400-66788400	Weak transcription	Gastric	stomach
28	chr7:66781400-66788800	Weak transcription	Esophagus	oesophagus
29	chr7:66781400-66792200	Weak transcription	Brain Germinal Matrix	brain
30	chr7:66781400-66810200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:66782200-66788200	Weak transcription	Ovary	ovary
32	chr7:66782600-66804600	Weak transcription	Brain Substantia Nigra	brain
33	chr7:66782800-66787800	Weak transcription	Thymus	Thymus
34	chr7:66782800-66788200	Weak transcription	Lung	lung
35	chr7:66782800-66788600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:66782800-66791600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr7:66782800-66804400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr7:66782800-66804400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr7:66782800-66809400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:66783000-66786800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:66783000-66790000	Weak transcription	Right Ventricle	heart
42	chr7:66783000-66792000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr7:66783000-66804400	Weak transcription	Left Ventricle	heart
44	chr7:66783000-66804600	Weak transcription	Brain Angular Gyrus	brain
45	chr7:66783200-66789200	Weak transcription	Spleen	Spleen
46	chr7:66783200-66789800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr7:66783400-66787400	Weak transcription	Fetal Thymus	thymus
48	chr7:66783400-66788200	Weak transcription	Primary T cells from cord blood	blood
49	chr7:66783400-66788600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:66783400-66789400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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