Variant report

Variant	rs861574
Chromosome Location	chr1:184721394-184721395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:183996674..183999449-chr1:184721278..184723656,2	K562	blood:
2	chr1:184721288..184723463-chr1:185282046..185283828,2	K562	blood:
3	chr1:184702525..184704823-chr1:184721375..184723068,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1061508	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs1062994	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10911631	0.83[ASN][1000 genomes]
rs10911633	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10911634	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10911636	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10911644	0.82[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10911645	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12031028	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12124929	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12126231	0.91[ASN][1000 genomes]
rs12131285	1.00[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.82[ASN][1000 genomes]
rs12133128	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12184284	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12567225	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12567226	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2064605	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2333715	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4651230	0.82[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MKK][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs481215	0.82[ASW][hapmap]
rs484847	0.82[ASW][hapmap]
rs543912	1.00[ASW][hapmap]
rs549088	0.82[ASW][hapmap]
rs641337	1.00[ASW][hapmap]
rs67359172	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs726427	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs861576	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs861578	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs861581	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs861583	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9425338	0.82[ASN][1000 genomes]
rs9425340	0.83[ASN][1000 genomes]
rs9425343	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9425632	0.82[ASN][1000 genomes]
rs9425634	0.82[ASN][1000 genomes]
rs971081	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS 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	69 gene(s)	inside rSNPs	diseases
3	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1009529	chr1:184663898-184731215	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs861574	OCLM	cis	parietal	SCAN
rs861574	PRG4	cis	parietal	SCAN
rs861574	EDEM3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184674600-184723000	Weak transcription	Aorta	Aorta
2	chr1:184677600-184723200	Weak transcription	Lung	lung
3	chr1:184685000-184721800	Weak transcription	Fetal Heart	heart
4	chr1:184685400-184722800	Weak transcription	Ovary	ovary
5	chr1:184685600-184722600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:184686200-184722600	Weak transcription	Brain Germinal Matrix	brain
7	chr1:184690400-184721800	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:184698200-184722800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:184699800-184722200	Weak transcription	Fetal Stomach	stomach
10	chr1:184701600-184721800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:184702200-184721800	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:184702200-184721800	Weak transcription	NH-A	brain
13	chr1:184702200-184722200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:184703200-184721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:184703200-184722800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:184703400-184721400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:184704600-184721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:184705000-184721800	Weak transcription	NHEK	skin
19	chr1:184706200-184722400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:184706800-184721800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:184706800-184721800	Weak transcription	Osteobl	bone
22	chr1:184707000-184721800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:184707000-184723000	Weak transcription	Placenta	Placenta
24	chr1:184707200-184722600	Weak transcription	HSMM	muscle
25	chr1:184712000-184722800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:184712400-184721800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:184712600-184722600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:184715000-184722800	Weak transcription	Fetal Brain Male	brain
29	chr1:184715400-184721800	Weak transcription	Brain Substantia Nigra	brain
30	chr1:184715400-184722600	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:184715600-184721400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:184715600-184721800	Weak transcription	Brain Angular Gyrus	brain
33	chr1:184715600-184721800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:184715800-184721800	Weak transcription	Brain Anterior Caudate	brain
35	chr1:184715800-184721800	Weak transcription	Fetal Kidney	kidney
36	chr1:184715800-184722000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:184715800-184722200	Weak transcription	NHLF	lung
38	chr1:184715800-184722600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:184716000-184721800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:184716000-184721800	Weak transcription	HUVEC	blood vessel
41	chr1:184716000-184722600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:184716600-184721600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:184716600-184721800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:184716600-184722400	Weak transcription	Fetal Thymus	thymus
45	chr1:184717000-184721400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:184717000-184721400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:184717000-184721400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:184717000-184721400	Weak transcription	Adipose Nuclei	Adipose
49	chr1:184717000-184721800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr1:184717200-184721400	Weak transcription	Rectal Mucosa Donor 29	rectum

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