Variant report

Variant	rs16894091
Chromosome Location	chr6:28390137-28390138
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28356707..28359445-chr6:28388134..28391982,4	K562	blood:
2	chr6:28389572..28392930-chr6:28395042..28397704,3	K562	blood:
3	chr6:28356866..28359445-chr6:28388346..28391982,3	K562	blood:
4	chr6:28385891..28388590-chr6:28390011..28392158,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1005126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10807030	0.82[ASN][1000 genomes]
rs10807031	0.82[ASN][1000 genomes]
rs11751928	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs11752919	0.83[ASW][hapmap]
rs11755387	0.91[CHB][hapmap]
rs11756111	0.84[LWK][hapmap]
rs13190937	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13193272	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196606	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13199081	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13203055	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209596	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13215804	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13217326	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1474589	0.81[ASW][hapmap]
rs16894011	0.91[CHB][hapmap]
rs16894106	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16894116	0.81[CEU][hapmap]
rs16901847	0.81[CEU][hapmap]
rs17856167	0.91[CHB][hapmap]
rs2021745	0.80[LWK][hapmap]
rs2071965	0.83[ASW][hapmap];0.85[MEX][hapmap]
rs2108923	0.82[ASN][1000 genomes]
rs2232427	0.91[CHB][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2531813	0.80[LWK][hapmap]
rs28505234	0.86[ASN][1000 genomes]
rs2859372	0.80[LWK][hapmap]
rs35908902	0.82[ASN][1000 genomes]
rs3799499	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3799500	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs3800328	0.94[ASW][hapmap];0.85[MEX][hapmap]
rs4254981	0.88[ASW][hapmap];0.81[MEX][hapmap]
rs57071502	0.86[ASN][1000 genomes]
rs58020991	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6899389	0.88[ASW][hapmap];0.81[MEX][hapmap]
rs6902687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6905380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6922169	0.88[ASW][hapmap];0.81[MEX][hapmap]
rs6928773	0.83[ASW][hapmap];0.81[MEX][hapmap]
rs6931359	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6940744	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71559081	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740429	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750526	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7754960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7774981	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468356	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs9468358	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9468364	0.90[CHB][hapmap]
rs9969098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv1836974	chr6:28376981-28398748	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs16894091	NKAPL	cis	parietal	SCAN
rs16894091	ZNF187	cis	cerebellum	SCAN
rs16894091	HLA-H	cis	multi-tissue	Pritchard
rs16894091	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs16894091	BTN3A2	cis	multi-tissue	Pritchard
rs16894091	ZSCAN23	cis	parietal	SCAN
rs16894091	ZSCAN23	cis	Artery Tibial	GTEx
rs16894091	ZSCAN23	cis	cerebellum	SCAN
rs16894091	TRIM38	cis	cerebellum	SCAN
rs16894091	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs16894091	AL022393.7	cis	Muscle Skeletal	GTEx
rs16894091	HLA-A	cis	multi-tissue	Pritchard
rs16894091	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs16894091	ZNF192	cis	cerebellum	SCAN
rs16894091	ZNF323	cis	parietal	SCAN
rs16894091	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28371200-28410400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:28377600-28390200	Weak transcription	Fetal Lung	lung
3	chr6:28380800-28390600	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:28383400-28390600	Weak transcription	Fetal Stomach	stomach
5	chr6:28383600-28392600	Weak transcription	Brain Germinal Matrix	brain
6	chr6:28383800-28393000	Weak transcription	Fetal Intestine Small	intestine
7	chr6:28384600-28390200	Weak transcription	NH-A	brain
8	chr6:28384600-28410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:28384800-28390800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:28385000-28390600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:28385200-28390600	Weak transcription	Placenta	Placenta
12	chr6:28385400-28391000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:28385400-28391200	Weak transcription	HSMMtube	muscle
14	chr6:28385400-28402000	Weak transcription	Fetal Kidney	kidney
15	chr6:28385400-28402200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:28385600-28390800	Weak transcription	Aorta	Aorta
17	chr6:28385600-28390800	Weak transcription	Ovary	ovary
18	chr6:28385600-28410800	Weak transcription	Lung	lung
19	chr6:28385800-28390800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:28385800-28391800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:28386000-28402200	Weak transcription	Osteobl	bone
22	chr6:28386000-28410400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:28386200-28390600	Weak transcription	Right Ventricle	heart
24	chr6:28386200-28391000	Weak transcription	Psoas Muscle	Psoas
25	chr6:28386200-28395800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:28386600-28391000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:28386600-28392200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:28386600-28392800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:28386600-28397800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:28386800-28392000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:28386800-28393600	Weak transcription	Fetal Heart	heart
32	chr6:28386800-28402200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr6:28387400-28390600	Weak transcription	Fetal Intestine Large	intestine
34	chr6:28387600-28393000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:28387600-28394200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:28387800-28390600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr6:28387800-28390600	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:28387800-28390800	Weak transcription	Brain Anterior Caudate	brain
39	chr6:28387800-28393000	Weak transcription	Fetal Brain Male	brain
40	chr6:28387800-28395400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:28387800-28410200	Weak transcription	Brain Angular Gyrus	brain
42	chr6:28388000-28392800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr6:28388000-28410400	Weak transcription	NHDF-Ad	bronchial
44	chr6:28388400-28390600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:28388400-28393000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:28388400-28399200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:28388800-28390800	Weak transcription	Left Ventricle	heart
48	chr6:28389000-28391200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:28389000-28391800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:28389000-28392600	Weak transcription	Primary hematopoietic stem cells	blood

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