Variant report

Variant	rs7539544
Chromosome Location	chr1:70831841-70831842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTH-9	chr1:70831829-70831920	NONHSAT003856

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10465863	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10889868	0.81[CHD][hapmap]
rs11209599	1.00[CEU][hapmap]
rs11209600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11209602	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11209603	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11209608	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11209611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11800138	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12028257	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12029977	0.82[AMR][1000 genomes]
rs12030275	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12031053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12034101	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12036256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12037272	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12042565	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12565458	0.93[AMR][1000 genomes]
rs12565460	0.91[AMR][1000 genomes]
rs1327873	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17131276	0.83[CEU][hapmap];0.91[AMR][1000 genomes]
rs17131285	0.83[CEU][hapmap];0.91[AMR][1000 genomes]
rs1969953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4560989	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4650038	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4650041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4650047	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56211824	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58997663	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59821213	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60602940	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61122312	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61587863	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61678482	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6686181	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72678630	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72678644	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72678645	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72678646	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72680732	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs768433	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs998523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7539544	SFRS11	Cis_1M	lymphoblastoid	RTeQTL
rs7539544	HHLA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70821000-70835200	Weak transcription	Pancreas	Pancrea
2	chr1:70821000-70836400	Weak transcription	Left Ventricle	heart
3	chr1:70821000-70838400	Weak transcription	Lung	lung
4	chr1:70821200-70832000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:70821200-70833600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:70821200-70835200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:70821200-70836800	Weak transcription	Fetal Stomach	stomach
8	chr1:70821200-70841400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:70821400-70832600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:70821400-70832600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:70821400-70838000	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:70821600-70834800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:70821600-70836400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:70821600-70839000	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:70822000-70834000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:70822000-70836400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:70822000-70839400	Weak transcription	Brain Substantia Nigra	brain
18	chr1:70822200-70835600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:70822400-70834600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:70824800-70833000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:70825000-70836800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:70826000-70832600	Weak transcription	HMEC	breast
23	chr1:70826000-70833000	Weak transcription	Liver	Liver
24	chr1:70826200-70832600	Weak transcription	NHEK	skin
25	chr1:70826600-70832600	Weak transcription	Ovary	ovary
26	chr1:70827800-70838400	Weak transcription	Fetal Lung	lung
27	chr1:70827800-70839800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:70828000-70838200	Weak transcription	Adipose Nuclei	Adipose
29	chr1:70828400-70833000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:70828400-70841000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:70829200-70838000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:70831400-70832000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr1:70831400-70832000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:70831400-70832200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:70831600-70832000	Enhancers	HUES6 Cell Line	embryonic stem cell

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