Variant report

Variant	rs7754960
Chromosome Location	chr6:28346945-28346946
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28336184..28339998-chr6:28343727..28348047,5	K562	blood:
2	chr6:28340056..28341598-chr6:28344823..28347301,2	K562	blood:
3	chr6:28346545..28348363-chr6:28349584..28351262,2	MCF-7	breast:
4	chr6:28336184..28339617-chr6:28343727..28347086,4	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1005126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11751928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11755387	0.92[CHB][hapmap]
rs12697938	0.80[YRI][hapmap]
rs13190937	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs13193272	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13196606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13199081	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13203055	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13209596	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13215804	1.00[CHB][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs13217326	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1416918	0.80[YRI][hapmap]
rs1591913	0.80[YRI][hapmap]
rs16894011	0.91[CHB][hapmap]
rs16894091	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16894106	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17856167	0.92[CHB][hapmap]
rs2232427	0.92[CHB][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505234	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3799499	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57071502	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58020991	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6902687	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6905380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6931359	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6940744	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71559081	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7740429	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7750526	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7759191	0.80[YRI][hapmap]
rs7774981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461459	0.80[YRI][hapmap]
rs9468356	0.85[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9468358	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9468364	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs9468368	0.80[YRI][hapmap]
rs9969098	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7754960	ZSCAN23	cis	Artery Tibial	GTEx
rs7754960	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs7754960	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs7754960	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs7754960	AL022393.7	cis	Muscle Skeletal	GTEx
rs7754960	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs7754960	AL022393.7	cis	Heart Left Ventricle	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28318400-28350800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:28324400-28347600	Weak transcription	NHDF-Ad	bronchial
3	chr6:28324400-28347800	Weak transcription	Fetal Brain Male	brain
4	chr6:28324400-28348200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:28324600-28349400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:28324600-28349600	Weak transcription	NHEK	skin
9	chr6:28324600-28358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:28325400-28350800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:28332000-28350600	Weak transcription	Psoas Muscle	Psoas
12	chr6:28333800-28347800	Weak transcription	HUVEC	blood vessel
13	chr6:28333800-28348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:28333800-28349800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:28333800-28349800	Weak transcription	Pancreas	Pancrea
16	chr6:28333800-28350800	Weak transcription	Lung	lung
17	chr6:28333800-28351000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:28334000-28348000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:28334000-28350000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:28334000-28350600	Weak transcription	Colonic Mucosa	Colon
21	chr6:28334000-28350800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:28334200-28347800	Weak transcription	NHLF	lung
23	chr6:28334200-28348000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:28334200-28348000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:28334200-28348200	Weak transcription	Brain Substantia Nigra	brain
26	chr6:28334200-28348800	Weak transcription	Fetal Heart	heart
27	chr6:28334200-28349400	Weak transcription	Right Ventricle	heart
28	chr6:28334200-28349800	Weak transcription	Aorta	Aorta
29	chr6:28334200-28351000	Weak transcription	Gastric	stomach
30	chr6:28334200-28351200	Weak transcription	Spleen	Spleen
31	chr6:28334400-28347200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:28334400-28347400	Weak transcription	HSMM	muscle
33	chr6:28334400-28347600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:28334400-28347800	Weak transcription	Brain Angular Gyrus	brain
35	chr6:28334400-28347800	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:28334400-28348000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:28334400-28348000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr6:28334400-28348000	Weak transcription	Thymus	Thymus
39	chr6:28334400-28348000	Weak transcription	HSMMtube	muscle
40	chr6:28334400-28350600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:28334400-28351000	Weak transcription	Esophagus	oesophagus
42	chr6:28334600-28347200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:28334600-28347600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:28334600-28347600	Weak transcription	Osteobl	bone
45	chr6:28334600-28347800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr6:28334600-28347800	Weak transcription	A549	lung
47	chr6:28334600-28351000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:28334800-28347800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:28334800-28347800	Weak transcription	Placenta	Placenta
50	chr6:28334800-28348000	Weak transcription	HepG2	liver

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