Variant report

Variant	rs971081
Chromosome Location	chr1:184716457-184716458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184709738..184712321-chr1:184713250..184716697,3	K562	blood:
2	chr1:184708973..184712904-chr1:184713895..184716754,5	K562	blood:
3	chr1:184708169..184713415-chr1:184713456..184716461,4	MCF-7	breast:
4	chr1:184687896..184689795-chr1:184715143..184716835,2	MCF-7	breast:
5	chr1:184715138..184717798-chr17:57916015..57918507,3	MCF-7	breast:
6	chr1:184708584..184710764-chr1:184716187..184718399,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1061508	1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap]
rs1062994	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911631	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10911633	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911634	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911636	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911644	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10911645	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12031028	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12032144	0.81[AMR][1000 genomes]
rs12071631	0.87[GIH][hapmap]
rs12124929	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12126231	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12131285	0.82[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12133128	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12137438	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12184284	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12567225	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12567226	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2024767	0.87[GIH][hapmap]
rs2064605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2333715	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2333716	0.87[GIH][hapmap]
rs2877994	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3736757	0.87[GIH][hapmap]
rs3895196	0.81[GIH][hapmap]
rs4233120	0.81[AMR][1000 genomes]
rs4651230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs543912	0.82[ASW][hapmap]
rs641337	0.82[ASW][hapmap]
rs6663178	0.85[GIH][hapmap]
rs67359172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726427	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs861574	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs861575	0.87[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs861576	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs861577	0.80[EUR][1000 genomes]
rs861578	0.95[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs861581	0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs861583	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9425338	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9425340	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9425343	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425632	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9425634	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	esv1849889	chr1:184667371-184718601	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv872584	chr1:184678290-184716457	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs971081	EDEM3	cis	Esophagus Muscularis	GTEx
rs971081	FAM129A	cis	cerebellum	SCAN
rs971081	PRG4	cis	parietal	SCAN
rs971081	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs971081	C1orf200	trans	cerebellum	SCAN

Chromatin state (count:88 , 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	chr1:184685600-184721000	Weak transcription	Right Ventricle	heart
6	chr1:184685600-184722600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:184686200-184722600	Weak transcription	Brain Germinal Matrix	brain
8	chr1:184690400-184721800	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:184698200-184722800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:184699800-184722200	Weak transcription	Fetal Stomach	stomach
11	chr1:184701600-184721800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:184702200-184721800	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:184702200-184721800	Weak transcription	NH-A	brain
14	chr1:184702200-184722200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:184703200-184721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:184703200-184722800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:184703400-184721400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:184703600-184720800	Weak transcription	Pancreas	Pancrea
19	chr1:184704600-184721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:184705000-184716800	Weak transcription	Left Ventricle	heart
21	chr1:184705000-184721800	Weak transcription	NHEK	skin
22	chr1:184706200-184722400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:184706800-184721800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:184706800-184721800	Weak transcription	Osteobl	bone
25	chr1:184707000-184721800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:184707000-184723000	Weak transcription	Placenta	Placenta
27	chr1:184707200-184722600	Weak transcription	HSMM	muscle
28	chr1:184710800-184716800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr1:184710800-184717000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:184710800-184719600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:184711000-184716800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr1:184712000-184722800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:184712400-184721800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:184712600-184722600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:184713000-184717200	Enhancers	Primary T cells from cord blood	blood
36	chr1:184713600-184716800	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr1:184713800-184717000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:184714400-184717000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:184714600-184716600	Strong transcription	Fetal Thymus	thymus
40	chr1:184714800-184716600	Enhancers	Primary hematopoietic stem cells	blood
41	chr1:184715000-184716600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:184715000-184722800	Weak transcription	Fetal Brain Male	brain
43	chr1:184715200-184717200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:184715400-184716800	Strong transcription	NHDF-Ad	bronchial
45	chr1:184715400-184717200	Enhancers	Stomach Mucosa	stomach
46	chr1:184715400-184717400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:184715400-184717600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:184715400-184721800	Weak transcription	Brain Substantia Nigra	brain
49	chr1:184715400-184722600	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:184715600-184716800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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