Variant report

Variant	rs1411701
Chromosome Location	chr1:94635028-94635029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94634875..94637097-chr1:94638561..94641795,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABCA4-1	chr1:94634465-94637015	NONHSAT004576

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10443184	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1048866	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782980	0.82[EUR][1000 genomes]
rs10874840	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11165090	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411698	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1411700	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929130	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2781572	0.85[GIH][hapmap];0.80[TSI][hapmap]
rs35791244	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3789687	0.83[EUR][1000 genomes]
rs3814020	0.81[EUR][1000 genomes]
rs4847294	0.85[GIH][hapmap];0.83[TSI][hapmap]
rs6541340	0.84[ASW][hapmap];0.84[CEU][hapmap];0.87[GIH][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6541411	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6657063	0.85[GIH][hapmap];0.83[TSI][hapmap]
rs6674226	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6691702	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7536759	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7551045	0.84[GIH][hapmap]
rs951534	0.85[GIH][hapmap];0.80[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871416	chr1:94566311-94635028	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1411701	SLC44A3	cis	parietal	SCAN
rs1411701	HSP90B3P	cis	parietal	SCAN
rs1411701	HFM1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94626600-94635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:94626800-94635200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:94626800-94636800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:94626800-94636800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:94626800-94639200	Weak transcription	NHLF	lung
6	chr1:94626800-94639400	Weak transcription	Psoas Muscle	Psoas
7	chr1:94626800-94639400	Weak transcription	NHEK	skin
8	chr1:94626800-94643400	Weak transcription	Fetal Heart	heart
9	chr1:94627000-94636200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:94627000-94639400	Weak transcription	HSMMtube	muscle
11	chr1:94629800-94639400	Weak transcription	Spleen	Spleen
12	chr1:94630800-94639400	Weak transcription	Gastric	stomach
13	chr1:94631400-94639400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:94631800-94636600	Weak transcription	Fetal Kidney	kidney
15	chr1:94631800-94639800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:94631800-94646600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:94632200-94639400	Weak transcription	Pancreas	Pancrea
18	chr1:94632400-94636200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:94633000-94636200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:94633200-94639400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:94633400-94636200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:94633400-94636600	Weak transcription	Adipose Nuclei	Adipose
23	chr1:94633400-94639400	Weak transcription	Left Ventricle	heart
24	chr1:94633600-94637000	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:94634000-94639400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:94634200-94643000	Strong transcription	HUVEC	blood vessel
27	chr1:94634200-94656600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:94634200-94658400	Strong transcription	HSMM	muscle
29	chr1:94634200-94660800	Strong transcription	NH-A	brain
30	chr1:94634200-94661800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:94634200-94675200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:94634400-94636000	Weak transcription	Liver	Liver
33	chr1:94634400-94639400	Weak transcription	A549	lung
34	chr1:94634400-94646400	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr1:94634400-94646600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:94634400-94660400	Strong transcription	NHDF-Ad	bronchial
37	chr1:94634600-94639400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:94634600-94639400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:94634600-94662000	Strong transcription	HMEC	breast
40	chr1:94634800-94644400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:94634800-94645000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:94635000-94635800	Weak transcription	Osteobl	bone
43	chr1:94635000-94636600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr1:94635000-94637000	Weak transcription	Lung	lung
45	chr1:94635000-94646800	Weak transcription	Esophagus	oesophagus
46	chr1:94635000-94658000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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