Variant report

Variant	rs6111004
Chromosome Location	chr20:16256637-16256638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10485549	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10485550	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11907241	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11908227	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11908242	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16997595	1.00[JPT][hapmap]
rs17730831	1.00[ASN][1000 genomes]
rs17730901	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17731020	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144896	0.82[CHB][hapmap]
rs3848791	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848792	1.00[ASN][1000 genomes]
rs3848793	1.00[ASN][1000 genomes]
rs4052895	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276366	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287828	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4416282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814466	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814467	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57988134	1.00[ASN][1000 genomes]
rs6105560	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105561	1.00[ASN][1000 genomes]
rs6105562	1.00[ASN][1000 genomes]
rs6105564	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs6110998	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6110999	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6111001	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111012	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6111025	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs718610	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs878582	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs878583	0.94[AMR][1000 genomes];0.99[EUR][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	nsv833930	chr20:16134347-16302763	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6111004	LOC100130264	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16242400-16275000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:16247600-16290800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr20:16248400-16259400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:16248400-16260800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr20:16248400-16261000	Weak transcription	Left Ventricle	heart
6	chr20:16248400-16263200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:16248400-16263800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr20:16248600-16291400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:16248800-16267000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr20:16248800-16272600	Weak transcription	Primary T cells from cord blood	blood
11	chr20:16249000-16272800	Weak transcription	Right Ventricle	heart
12	chr20:16249200-16277400	Weak transcription	Brain Substantia Nigra	brain
13	chr20:16249400-16264000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr20:16250000-16266800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr20:16250600-16260600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:16250800-16263400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr20:16251000-16265000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr20:16251400-16263000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr20:16251400-16263800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr20:16251600-16258200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr20:16251800-16256800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr20:16252000-16270800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr20:16252000-16289400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr20:16252400-16264400	Weak transcription	Small Intestine	intestine
25	chr20:16252400-16283000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr20:16252800-16264800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr20:16253000-16260800	Weak transcription	Psoas Muscle	Psoas
28	chr20:16253000-16277800	Weak transcription	Brain Angular Gyrus	brain
29	chr20:16253400-16256800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr20:16253600-16268200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr20:16253800-16257200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr20:16254000-16259600	Weak transcription	HepG2	liver
33	chr20:16254000-16263200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr20:16254000-16263200	Weak transcription	Fetal Stomach	stomach
35	chr20:16254000-16263800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr20:16254000-16264000	Weak transcription	Aorta	Aorta
37	chr20:16254000-16264400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr20:16254000-16265200	Weak transcription	NHEK	skin
39	chr20:16254000-16278800	Weak transcription	Adipose Nuclei	Adipose
40	chr20:16254000-16281400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr20:16254000-16290800	Weak transcription	Esophagus	oesophagus
42	chr20:16254000-16298400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr20:16254200-16258000	Weak transcription	Brain Hippocampus Middle	brain
44	chr20:16254200-16262400	Weak transcription	Gastric	stomach
45	chr20:16254200-16278600	Weak transcription	Pancreas	Pancrea
46	chr20:16254200-16284200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr20:16254400-16258200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr20:16254400-16263000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr20:16254600-16262000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr20:16254600-16264000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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