Variant report

Variant	rs1933934
Chromosome Location	chr1:47034928-47034929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47027680..47030218-chr1:47031436..47035434,3	K562	blood:
2	chr1:47033343..47035201-chr1:47067108..47069992,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DMBX1-2	chr1:47034154-47035926	ENSG00000235894
2	lnc-DMBX1-2	chr1:47034154-47035927	ENSG00000269956.1

Variant related genes	Relation type
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1054743	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10890405	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11211306	0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11211309	0.85[CHB][hapmap]
rs11211312	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11211317	0.82[EUR][1000 genomes]
rs11211328	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12029680	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs12047046	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12048342	0.91[EUR][1000 genomes]
rs12093643	0.82[EUR][1000 genomes]
rs12138971	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2181414	0.82[CHD][hapmap]
rs3753359	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3766231	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3766236	0.82[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs3766240	0.82[CEU][hapmap];0.90[CHB][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3818323	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55680528	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56869893	0.80[EUR][1000 genomes]
rs59446321	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6429606	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7543083	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs7552833	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7556307	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7556481	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs764803	0.83[EUR][1000 genomes]
rs8602	0.90[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs9659890	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9804164	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9804165	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1009899	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv534954	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv1011892	chr1:47010519-47067492	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1933934	ATPAF1	cis	multi-tissue	Pritchard
rs1933934	MPL	cis	parietal	SCAN
rs1933934	MKNK1	cis	Whole Blood	GTEx
rs1933934	C1orf84	cis	cerebellum	SCAN
rs1933934	C1orf223	cis	parietal	SCAN
rs1933934	MKNK1	cis	multi-tissue	Pritchard
rs1933934	MKNK1	cis	lung	GTEx
rs1933934	MKNK1	cis	cerebellum	SCAN
rs1933934	MOB3C	cis	Whole Blood	GTEx
rs1933934	CLDN19	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46999600-47035000	Weak transcription	Right Atrium	heart
2	chr1:47015800-47041200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:47015800-47043400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:47016000-47037400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:47017600-47039800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:47019800-47043600	Weak transcription	Dnd41	blood
7	chr1:47020800-47047400	Weak transcription	Brain Germinal Matrix	brain
8	chr1:47021000-47057000	Weak transcription	Fetal Brain Male	brain
9	chr1:47021200-47045000	Weak transcription	K562	blood
10	chr1:47021800-47054600	Weak transcription	A549	lung
11	chr1:47022200-47043400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:47022400-47053600	Strong transcription	Thymus	Thymus
13	chr1:47022600-47051400	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:47022600-47051600	Strong transcription	Liver	Liver
15	chr1:47023000-47039200	Strong transcription	Fetal Intestine Small	intestine
16	chr1:47023000-47044200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:47023000-47047400	Strong transcription	Primary T cells from cord blood	blood
18	chr1:47023200-47036400	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:47023200-47036600	Strong transcription	Ovary	ovary
20	chr1:47023200-47036800	Strong transcription	Pancreas	Pancrea
21	chr1:47023200-47044400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr1:47023200-47046600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:47023200-47047200	Strong transcription	Fetal Thymus	thymus
24	chr1:47023200-47051200	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:47023200-47060000	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:47023400-47038400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:47023400-47044600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:47023800-47045200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:47023800-47053200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:47024000-47054800	Weak transcription	HUVEC	blood vessel
31	chr1:47024600-47042400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:47025000-47041600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:47025400-47035000	Strong transcription	NHEK	skin
34	chr1:47025600-47062400	Weak transcription	Fetal Heart	heart
35	chr1:47027000-47041000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:47027200-47035200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:47027200-47047600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:47027600-47043400	Weak transcription	HepG2	liver
39	chr1:47027800-47037400	Weak transcription	HSMMtube	muscle
40	chr1:47028600-47035200	Strong transcription	Primary B cells from cord blood	blood
41	chr1:47028600-47036000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:47028800-47041000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:47028800-47043600	Weak transcription	HMEC	breast
44	chr1:47028800-47044800	Weak transcription	Stomach Mucosa	stomach
45	chr1:47029000-47041800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:47029200-47042200	Weak transcription	NHLF	lung
47	chr1:47030800-47035000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:47030800-47041000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:47030800-47046000	Weak transcription	Psoas Muscle	Psoas
50	chr1:47031000-47035000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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