Variant report

Variant	rs3737136
Chromosome Location	chr1:113060432-113060433
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	chr1:113059419..113061818-chr1:113160250..113161994,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ST7L-4	chr1:113060421-113061063	ENSG00000273483.1

Variant related genes	Relation type
ENSG00000116489	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10857961	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10857964	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10857967	0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1106287	0.94[CEU][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs11102496	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11102498	0.82[EUR][1000 genomes]
rs11102501	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11102509	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11102513	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs11102514	0.94[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs11102522	0.82[YRI][hapmap]
rs12029985	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12030612	0.82[AFR][1000 genomes]
rs12030641	0.82[AFR][1000 genomes]
rs12040988	0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12045227	0.95[AFR][1000 genomes]
rs12049572	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12117479	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12120956	0.93[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs12122980	0.94[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs12130243	0.94[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12137269	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12140506	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12406530	0.80[EUR][1000 genomes]
rs12724928	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12728311	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12756815	0.88[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17030613	1.00[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2009056	0.82[AFR][1000 genomes]
rs2064711	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2273368	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306937	0.84[AFR][1000 genomes]
rs2306940	0.94[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs2887882	0.87[AFR][1000 genomes]
rs34107138	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34569066	1.00[AFR][1000 genomes]
rs35023236	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35147679	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748656	0.84[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs3790598	0.81[TSI][hapmap]
rs3790606	0.91[CHB][hapmap]
rs3790609	0.81[TSI][hapmap]
rs3795819	0.94[CEU][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs55652172	1.00[AFR][1000 genomes]
rs56135413	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60900293	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61818802	0.82[AFR][1000 genomes]
rs6679	0.94[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs9308256	0.95[AFR][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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3737136	SYT6	cis	parietal	SCAN
rs3737136	ST7L	cis	Lymphoblastoid	GTEx
rs3737136	ST7L	cis	multi-tissue	Pritchard
rs3737136	SLC16A4	cis	cerebellum	SCAN
rs3737136	WNT2B	cis	multi-tissue	Pritchard
rs3737136	DENND2C	cis	parietal	SCAN
rs3737136	WNT2B	cis	parietal	SCAN
rs3737136	ST7L	cis	lymphoblastoid	seeQTL
rs3737136	ST7L	cis	lesional skin	skin_eQTL
rs3737136	GSTM1	cis	parietal	SCAN
rs3737136	AMPD1	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113052000-113082600	Weak transcription	Brain Angular Gyrus	brain
2	chr1:113052200-113067600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:113052200-113093200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:113052400-113067000	Weak transcription	Adipose Nuclei	Adipose
5	chr1:113054600-113066800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:113055000-113067000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:113055800-113067200	Weak transcription	Fetal Lung	lung
8	chr1:113055800-113067600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:113055800-113085200	Weak transcription	Thymus	Thymus
10	chr1:113056000-113067600	Weak transcription	HUVEC	blood vessel
11	chr1:113056600-113066800	Weak transcription	Placenta	Placenta
12	chr1:113057000-113067000	Weak transcription	Colonic Mucosa	Colon
13	chr1:113057600-113067000	Weak transcription	Fetal Brain Female	brain
14	chr1:113057800-113066800	Weak transcription	Brain Germinal Matrix	brain
15	chr1:113057800-113067600	Weak transcription	Fetal Intestine Large	intestine
16	chr1:113057800-113069600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:113058200-113062800	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:113058200-113067400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:113058400-113065400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:113058400-113069600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:113058400-113086600	Weak transcription	A549	lung
22	chr1:113058600-113064800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:113058600-113065800	Strong transcription	Fetal Stomach	stomach
24	chr1:113058600-113067400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:113058600-113069400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:113058800-113060800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:113058800-113060800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:113058800-113062600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:113058800-113062800	Weak transcription	NHDF-Ad	bronchial
30	chr1:113058800-113064800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:113058800-113067200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:113058800-113119400	Weak transcription	HepG2	liver
33	chr1:113059000-113061000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:113059000-113062200	Weak transcription	Osteobl	bone
35	chr1:113059000-113062800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:113059000-113064800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:113059000-113064800	Weak transcription	NHLF	lung
38	chr1:113059000-113065200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:113059000-113067000	Weak transcription	Right Ventricle	heart
40	chr1:113059200-113060800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:113059200-113062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:113059200-113067600	Weak transcription	Primary T cells from cord blood	blood
43	chr1:113059200-113071600	Weak transcription	Hela-S3	cervix
44	chr1:113059400-113061400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr1:113059600-113060800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:113059600-113060800	Enhancers	K562	blood
47	chr1:113059600-113069600	Weak transcription	Spleen	Spleen
48	chr1:113059800-113061000	Enhancers	Left Ventricle	heart
49	chr1:113060000-113060800	Strong transcription	Brain Anterior Caudate	brain
50	chr1:113060000-113065200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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