Variant report

Variant	rs16846546
Chromosome Location	chr1:173860182-173860183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173859716..173863027-chr1:173865455..173870785,5	K562	blood:
2	chr1:173854070..173860394-chr1:173860539..173867294,11	MCF-7	breast:
3	chr1:173855077..173857182-chr1:173858771..173861573,3	K562	blood:
4	chr1:173853137..173856860-chr1:173858771..173862944,6	K562	blood:
5	chr1:173831191..173840458-chr1:173852193..173864862,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234741	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000208317	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs14262	0.86[ASW][hapmap];0.88[LWK][hapmap];0.80[YRI][hapmap]
rs16846418	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16846433	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]
rs16846478	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846561	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[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846593	0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs16846660	0.80[LWK][hapmap]
rs1885679	0.86[ASW][hapmap];0.86[LWK][hapmap];0.80[YRI][hapmap]
rs2065170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068871	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2146372	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227617	0.86[ASW][hapmap];0.88[LWK][hapmap];0.80[YRI][hapmap]
rs2235095	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2759328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791021	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791022	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs57022387	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58994962	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61262741	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61649485	0.84[ASN][1000 genomes]
rs6656255	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6685043	0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs6687429	0.80[LWK][hapmap]
rs6691053	0.82[CHB][hapmap];0.80[LWK][hapmap]
rs6696381	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6790	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941987	0.87[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs941988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9970048	1.00[EUR][1000 genomes];0.95[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16846546		cis	Lymphoblastoid	GTEx
rs16846546	PRDX6	cis	parietal	SCAN
rs16846546	SNORD80	cis	parietal	SCAN
rs16846546	CENPL	cis	lymphoblastoid	seeQTL
rs16846546	dJ383J4.3	cis	multi-tissue	Pritchard
rs16846546	SNORD78	cis	parietal	SCAN
rs16846546	SNORD79	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173838200-173866000	Weak transcription	Small Intestine	intestine
2	chr1:173838400-173860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:173839000-173862800	Weak transcription	HMEC	breast
4	chr1:173841000-173864400	Weak transcription	Fetal Heart	heart
5	chr1:173841000-173868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:173853400-173865200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:173855400-173863000	Weak transcription	NHEK	skin
8	chr1:173855400-173868000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:173855600-173866800	Weak transcription	Pancreas	Pancrea
10	chr1:173855600-173875400	Weak transcription	NH-A	brain
11	chr1:173855800-173860200	Weak transcription	Spleen	Spleen
12	chr1:173855800-173863400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:173855800-173873000	Weak transcription	Fetal Intestine Small	intestine
14	chr1:173855800-173880400	Weak transcription	Thymus	Thymus
15	chr1:173856000-173861600	Weak transcription	Gastric	stomach
16	chr1:173856000-173862400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:173856000-173864200	Weak transcription	Fetal Stomach	stomach
18	chr1:173856000-173864400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:173856000-173865400	Weak transcription	Esophagus	oesophagus
20	chr1:173856000-173868400	Weak transcription	Hela-S3	cervix
21	chr1:173856000-173868600	Weak transcription	Brain Angular Gyrus	brain
22	chr1:173856000-173869400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:173856000-173869800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:173856000-173872600	Weak transcription	Fetal Thymus	thymus
25	chr1:173856000-173883000	Weak transcription	Right Ventricle	heart
26	chr1:173856200-173860400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:173856200-173861000	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:173856200-173862000	Weak transcription	Aorta	Aorta
29	chr1:173856200-173862200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:173856200-173862600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:173856200-173862800	Weak transcription	K562	blood
32	chr1:173856200-173863400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:173856200-173863600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:173856200-173863600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:173856200-173864200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:173856200-173864800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:173856200-173865600	Weak transcription	Dnd41	blood
38	chr1:173856200-173866200	Weak transcription	GM12878-XiMat	blood
39	chr1:173856200-173867800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:173856200-173868800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:173856200-173868800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:173856200-173869800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:173856200-173872800	Weak transcription	Ovary	ovary
44	chr1:173856200-173875400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:173856200-173878400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:173856200-173880400	Weak transcription	Psoas Muscle	Psoas
47	chr1:173856400-173861600	Weak transcription	Fetal Lung	lung
48	chr1:173856400-173864200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:173856400-173867200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:173856400-173868200	Weak transcription	Rectal Smooth Muscle	rectum

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