Variant report

Variant	rs10874840
Chromosome Location	chr1:94636836-94636837
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	chr1:94635193..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: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10443184	0.84[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1048866	0.84[ASW][hapmap];0.88[CEU][hapmap];0.87[GIH][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10782980	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11165090	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11196	0.92[ASW][hapmap];0.88[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1411698	0.87[CEU][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1411700	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1411701	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1541098	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1929130	0.87[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35791244	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789687	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3814020	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6541340	1.00[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6541411	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6541412	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6674226	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6691702	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7536759	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10874840	SLC44A3	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94626800-94639200	Weak transcription	NHLF	lung
2	chr1:94626800-94639400	Weak transcription	Psoas Muscle	Psoas
3	chr1:94626800-94639400	Weak transcription	NHEK	skin
4	chr1:94626800-94643400	Weak transcription	Fetal Heart	heart
5	chr1:94627000-94639400	Weak transcription	HSMMtube	muscle
6	chr1:94629800-94639400	Weak transcription	Spleen	Spleen
7	chr1:94630800-94639400	Weak transcription	Gastric	stomach
8	chr1:94631400-94639400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:94631800-94639800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:94631800-94646600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:94632200-94639400	Weak transcription	Pancreas	Pancrea
12	chr1:94633200-94639400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:94633400-94639400	Weak transcription	Left Ventricle	heart
14	chr1:94633600-94637000	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:94634000-94639400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:94634200-94643000	Strong transcription	HUVEC	blood vessel
17	chr1:94634200-94656600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:94634200-94658400	Strong transcription	HSMM	muscle
19	chr1:94634200-94660800	Strong transcription	NH-A	brain
20	chr1:94634200-94661800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:94634200-94675200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:94634400-94639400	Weak transcription	A549	lung
23	chr1:94634400-94646400	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr1:94634400-94646600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:94634400-94660400	Strong transcription	NHDF-Ad	bronchial
26	chr1:94634600-94639400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:94634600-94639400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:94634600-94662000	Strong transcription	HMEC	breast
29	chr1:94634800-94644400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:94634800-94645000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:94635000-94637000	Weak transcription	Lung	lung
32	chr1:94635000-94646800	Weak transcription	Esophagus	oesophagus
33	chr1:94635000-94658000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:94635200-94638200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:94635200-94638800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:94635600-94639400	Weak transcription	Fetal Stomach	stomach
37	chr1:94635800-94637800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:94635800-94646200	Strong transcription	Osteobl	bone
39	chr1:94636000-94639400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:94636000-94658400	Strong transcription	Liver	Liver
41	chr1:94636200-94638000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:94636200-94641000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:94636200-94644000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:94636200-94673400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:94636400-94638400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:94636600-94637000	Strong transcription	Fetal Kidney	kidney
47	chr1:94636600-94637200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:94636600-94638000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr1:94636600-94641200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr1:94636600-94647400	Strong transcription	Adipose Nuclei	Adipose

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