Variant report

Variant	rs16843855
Chromosome Location	chr1:172087098-172087099
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172081759..172083633-chr1:172085857..172087985,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10489297	1.00[CHB][hapmap]
rs10910941	1.00[CHB][hapmap]
rs10914141	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11584955	1.00[CHB][hapmap]
rs11589142	1.00[CHB][hapmap]
rs12123334	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12129264	1.00[CHB][hapmap]
rs12145177	1.00[JPT][hapmap]
rs16843860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17277008	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17277127	1.00[CHB][hapmap]
rs17346438	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17346452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17346473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17350544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17350579	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17350586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17361789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17361920	1.00[CHB][hapmap]
rs17472925	1.00[JPT][hapmap]
rs2209096	1.00[CHB][hapmap]
rs2421990	1.00[CHB][hapmap]
rs2421991	1.00[CHB][hapmap]
rs4244192	0.86[YRI][hapmap]
rs4540689	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs593688	1.00[CHB][hapmap]
rs61807762	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61807763	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs628479	1.00[CHB][hapmap]
rs6694089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541042	1.00[YRI][hapmap];0.90[AFR][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	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16843855	POGK	cis	parietal	SCAN
rs16843855	GORAB	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172049400-172110800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:172052400-172091600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:172062400-172109200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:172069200-172102000	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:172077000-172096000	Weak transcription	Brain Substantia Nigra	brain
6	chr1:172077200-172110600	Weak transcription	Brain Angular Gyrus	brain
7	chr1:172077400-172099400	Weak transcription	Fetal Brain Female	brain
8	chr1:172079000-172090400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:172079400-172089800	Weak transcription	Fetal Stomach	stomach
10	chr1:172082000-172089600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:172085600-172087600	Enhancers	Primary T cells from cord blood	blood
12	chr1:172085600-172088000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:172085600-172088200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:172085600-172088200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:172085600-172097000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:172085800-172113400	Weak transcription	Pancreas	Pancrea
17	chr1:172086400-172087600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:172086400-172087800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr1:172086400-172087800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:172086400-172088000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:172086400-172088000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr1:172086400-172088000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:172086400-172088000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr1:172086400-172088000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:172086600-172087400	Enhancers	Primary B cells from peripheral blood	blood
26	chr1:172086600-172087400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr1:172086800-172087400	Flanking Active TSS	GM12878-XiMat	blood
28	chr1:172086800-172087400	Enhancers	NHEK	skin
29	chr1:172087000-172087200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:172087000-172087200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:172087000-172087200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:172087000-172087400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr1:172087000-172087400	Enhancers	HMEC	breast

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