Variant report

Variant	rs12044374
Chromosome Location	chr1:94635986-94635987
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	chr1:94635193..94637097-chr1:94638561..94640426,2	K562	blood:
2	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: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10443184	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs1048866	0.85[GIH][hapmap];0.83[TSI][hapmap]
rs11196	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs12724975	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12752790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576593	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2022397	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2781572	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4847291	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847293	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4847294	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657063	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6682445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12044374	SLC44A3	cis	parietal	SCAN
rs12044374	NENF	Cis_chr	lymphoblastoid	RTeQTL
rs12044374	AK074181	cis	multi-tissue	Pritchard

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94626800-94636800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:94626800-94636800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:94626800-94639200	Weak transcription	NHLF	lung
4	chr1:94626800-94639400	Weak transcription	Psoas Muscle	Psoas
5	chr1:94626800-94639400	Weak transcription	NHEK	skin
6	chr1:94626800-94643400	Weak transcription	Fetal Heart	heart
7	chr1:94627000-94636200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:94627000-94639400	Weak transcription	HSMMtube	muscle
9	chr1:94629800-94639400	Weak transcription	Spleen	Spleen
10	chr1:94630800-94639400	Weak transcription	Gastric	stomach
11	chr1:94631400-94639400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:94631800-94636600	Weak transcription	Fetal Kidney	kidney
13	chr1:94631800-94639800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:94631800-94646600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:94632200-94639400	Weak transcription	Pancreas	Pancrea
16	chr1:94632400-94636200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:94633000-94636200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:94633200-94639400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:94633400-94636200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:94633400-94636600	Weak transcription	Adipose Nuclei	Adipose
21	chr1:94633400-94639400	Weak transcription	Left Ventricle	heart
22	chr1:94633600-94637000	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:94634000-94639400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:94634200-94643000	Strong transcription	HUVEC	blood vessel
25	chr1:94634200-94656600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:94634200-94658400	Strong transcription	HSMM	muscle
27	chr1:94634200-94660800	Strong transcription	NH-A	brain
28	chr1:94634200-94661800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:94634200-94675200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:94634400-94636000	Weak transcription	Liver	Liver
31	chr1:94634400-94639400	Weak transcription	A549	lung
32	chr1:94634400-94646400	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr1:94634400-94646600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:94634400-94660400	Strong transcription	NHDF-Ad	bronchial
35	chr1:94634600-94639400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:94634600-94639400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:94634600-94662000	Strong transcription	HMEC	breast
38	chr1:94634800-94644400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:94634800-94645000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:94635000-94636600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:94635000-94637000	Weak transcription	Lung	lung
42	chr1:94635000-94646800	Weak transcription	Esophagus	oesophagus
43	chr1:94635000-94658000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:94635200-94638200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:94635200-94638800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:94635600-94639400	Weak transcription	Fetal Stomach	stomach
47	chr1:94635800-94637800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:94635800-94646200	Strong transcription	Osteobl	bone

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