Variant report

Variant	rs351372
Chromosome Location	chr1:113059220-113059221
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113057544..113060149-chr1:113196498..113199134,2	K562	blood:
2	chr1:113057899..113060192-chr1:113160465..113162530,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116489	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1001494	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1006298	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10745330	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10776755	0.85[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs10776756	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10776757	0.85[CEU][hapmap]
rs10857963	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102497	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102512	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11584092	0.85[CEU][hapmap]
rs12046208	0.85[CEU][hapmap];0.83[GIH][hapmap];0.86[MKK][hapmap]
rs12126277	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12728001	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1994604	0.80[EUR][1000 genomes]
rs2932532	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs2932536	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs2999154	0.92[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.86[TSI][hapmap]
rs2999155	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs3013439	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs3013440	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs4838959	0.81[GIH][hapmap];0.84[TSI][hapmap]
rs4839254	0.81[CEU][hapmap]
rs6537743	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537748	0.81[GIH][hapmap]
rs6537749	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs6666579	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6669096	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6679414	0.80[AMR][1000 genomes]
rs6682737	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6691932	0.82[EUR][1000 genomes]
rs6700673	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs7415820	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs7513716	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544663	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7546094	0.80[EUR][1000 genomes]
rs7554345	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7554916	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs902289	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs910697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9429486	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1008375	chr1:113028271-113060221	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs351372	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs351372	ST7L	cis	lesional skin	skin_eQTL
rs351372	ST7L	cis	uninvolved skin	skin_eQTL
rs351372	WNT2B	cis	parietal	SCAN
rs351372	ST7L	cis	Adipose Subcutaneous	GTEx
rs351372	ST7L	cis	multi-tissue	Pritchard
rs351372	ST7L	cis	Nerve Tibial	GTEx
rs351372	ST7L	cis	Heart Left Ventricle	GTEx
rs351372	ST7L	cis	Thyroid	GTEx
rs351372	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs351372	ALX3	cis	parietal	SCAN
rs351372	ST7L	cis	Stomach	GTEx
rs351372	ST7L	cis	Esophagus Muscularis	GTEx
rs351372	ST7L	cis	lymphoblastoid	seeQTL
rs351372	C1orf162	cis	parietal	SCAN
rs351372	ST7L	cis	lung	GTEx
rs351372	ST7L	cis	Lymphoblastoid	GTEx
rs351372	ST7L	cis	normal skin	skin_eQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113051800-113059800	Weak transcription	Aorta	Aorta
2	chr1:113052000-113059600	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:113052000-113082600	Weak transcription	Brain Angular Gyrus	brain
4	chr1:113052200-113059600	Weak transcription	Pancreas	Pancrea
5	chr1:113052200-113067600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:113052200-113093200	Weak transcription	Brain Substantia Nigra	brain
7	chr1:113052400-113059400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:113052400-113067000	Weak transcription	Adipose Nuclei	Adipose
9	chr1:113053000-113059400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:113054600-113066800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:113055000-113059400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:113055000-113067000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:113055200-113059400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:113055800-113059600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:113055800-113067200	Weak transcription	Fetal Lung	lung
16	chr1:113055800-113067600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:113055800-113085200	Weak transcription	Thymus	Thymus
18	chr1:113056000-113059400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:113056000-113067600	Weak transcription	HUVEC	blood vessel
20	chr1:113056400-113059800	Weak transcription	Lung	lung
21	chr1:113056600-113066800	Weak transcription	Placenta	Placenta
22	chr1:113057000-113067000	Weak transcription	Colonic Mucosa	Colon
23	chr1:113057200-113060400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:113057400-113059600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:113057600-113067000	Weak transcription	Fetal Brain Female	brain
26	chr1:113057800-113060200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:113057800-113066800	Weak transcription	Brain Germinal Matrix	brain
28	chr1:113057800-113067600	Weak transcription	Fetal Intestine Large	intestine
29	chr1:113057800-113069600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:113058200-113059400	Weak transcription	Fetal Intestine Small	intestine
31	chr1:113058200-113059400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:113058200-113062800	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:113058200-113067400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:113058400-113060200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:113058400-113065400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:113058400-113069600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:113058400-113086600	Weak transcription	A549	lung
38	chr1:113058600-113059600	Strong transcription	Ovary	ovary
39	chr1:113058600-113059800	Weak transcription	Left Ventricle	heart
40	chr1:113058600-113064800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:113058600-113065800	Strong transcription	Fetal Stomach	stomach
42	chr1:113058600-113067400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:113058600-113069400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:113058800-113059800	Weak transcription	Right Atrium	heart
45	chr1:113058800-113060800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:113058800-113060800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:113058800-113062600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:113058800-113062800	Weak transcription	NHDF-Ad	bronchial
49	chr1:113058800-113064800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:113058800-113067200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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