Variant report

Variant	rs10874870
Chromosome Location	chr1:95101465-95101466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10782983	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs10782985	0.81[EUR][1000 genomes]
rs10874869	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10874872	0.86[ASN][1000 genomes]
rs11165184	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs1341643	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1341644	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2971937	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2996286	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3814018	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs3885983	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847319	0.85[ASN][1000 genomes]
rs4847325	0.83[EUR][1000 genomes]
rs6541357	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs715813	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7537169	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv519997	chr1:95083836-95113417	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1001230	chr1:95085184-95108531	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1910	chr1:95100383-95111872	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10874870	ABCD3	cis	cerebellum	SCAN
rs10874870	CNN3	cis	lymphoblastoid	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95090000-95102800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:95095800-95102200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:95095800-95108400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:95099000-95102000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:95099400-95102000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:95099400-95102800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:95099400-95102800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:95099600-95102200	Weak transcription	Ovary	ovary
9	chr1:95099600-95102800	Weak transcription	NHDF-Ad	bronchial
10	chr1:95099800-95111600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:95100000-95101800	Enhancers	K562	blood
12	chr1:95100000-95103200	Enhancers	NHEK	skin
13	chr1:95100200-95103000	Enhancers	HMEC	breast
14	chr1:95100400-95101600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:95100400-95101800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:95100400-95102000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:95100400-95102800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr1:95100400-95102800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:95100400-95103000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr1:95100400-95103200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr1:95100400-95103200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:95100400-95103400	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr1:95100600-95101800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:95100600-95102200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr1:95100600-95103000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:95100600-95103200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr1:95100600-95103200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:95100600-95103200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr1:95100800-95101800	Weak transcription	Stomach Mucosa	stomach
30	chr1:95100800-95101800	Weak transcription	NHLF	lung
31	chr1:95100800-95110600	Weak transcription	NH-A	brain
32	chr1:95100800-95112000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:95101000-95101800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:95101000-95103600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:95101400-95101800	Weak transcription	Pancreas	Pancrea
36	chr1:95101400-95102800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr1:95101400-95103200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:95101400-95103200	Enhancers	Hela-S3	cervix
39	chr1:95101400-95107200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:95101400-95107200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:95101400-95108200	Weak transcription	Placenta	Placenta

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