Variant report

Variant	rs16846433
Chromosome Location	chr1:173820593-173820594
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173793370..173795660-chr1:173820516..173822118,2	K562	blood:

Variant related genes	Relation type
ENSG00000120334	Chromatin interaction
ENSG00000117593	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs16846418	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16846478	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846526	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846546	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846561	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846593	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs2065170	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2068871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2146372	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2227589	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2227592	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2235095	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759328	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791021	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57022387	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58994962	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61262741	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61649485	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6656255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6685043	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs6696381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6790	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941987	0.87[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs941988	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9970048	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16846433	CENPL	cis	lymphoblastoid	seeQTL
rs16846433	dJ383J4.3	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
2	chr1:173794600-173820600	Weak transcription	NHLF	lung
3	chr1:173794600-173821800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:173794600-173821800	Weak transcription	Pancreas	Pancrea
5	chr1:173794600-173822000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:173794600-173832000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:173794600-173832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:173794600-173832600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
10	chr1:173794800-173834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:173795000-173826200	Weak transcription	Psoas Muscle	Psoas
12	chr1:173795000-173834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:173795200-173822400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:173795200-173824600	Weak transcription	Gastric	stomach
15	chr1:173797200-173828400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:173799600-173828800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:173801000-173822200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:173801200-173825000	Weak transcription	Brain Angular Gyrus	brain
19	chr1:173803000-173826600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:173806800-173822800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:173809000-173822000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:173809200-173825200	Weak transcription	NHDF-Ad	bronchial
23	chr1:173809800-173831800	Weak transcription	Colonic Mucosa	Colon
24	chr1:173810200-173822000	Weak transcription	Fetal Kidney	kidney
25	chr1:173811000-173824600	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:173811000-173825000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:173811200-173820600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:173811200-173822200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:173811200-173825000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:173811200-173829200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:173811400-173821400	Weak transcription	Osteobl	bone
32	chr1:173812000-173820600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:173813000-173822000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:173813200-173820600	Weak transcription	NHEK	skin
35	chr1:173813200-173821000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:173813200-173821400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:173813200-173822000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:173813200-173822000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:173813200-173822000	Weak transcription	HSMMtube	muscle
40	chr1:173813200-173823000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:173813200-173824800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:173813200-173831800	Weak transcription	Right Ventricle	heart
43	chr1:173813200-173832000	Weak transcription	Small Intestine	intestine
44	chr1:173813400-173820600	Weak transcription	HSMM	muscle
45	chr1:173813400-173821000	Weak transcription	Liver	Liver
46	chr1:173813400-173822000	Weak transcription	Primary B cells from cord blood	blood
47	chr1:173813400-173822000	Weak transcription	NH-A	brain
48	chr1:173813400-173831000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:173813600-173820600	Weak transcription	K562	blood
50	chr1:173813600-173821000	Weak transcription	Rectal Mucosa Donor 31	rectum

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