Variant report

Variant	rs1006298
Chromosome Location	chr1:113061959-113061960
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113061676..113064298-chr1:113066222..113068945,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1001494	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10745330	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10776755	0.85[CEU][hapmap]
rs10776756	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10776757	0.86[CEU][hapmap]
rs10857963	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11102497	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102512	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11584092	0.85[CEU][hapmap]
rs12046208	0.85[CEU][hapmap]
rs12126277	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12728001	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932532	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2932536	0.96[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap]
rs2999154	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]
rs2999155	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs3013439	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs3013440	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs351372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4839254	0.82[CEU][hapmap]
rs6537743	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6666579	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6669096	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6679414	0.80[AMR][1000 genomes]
rs6682737	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6691932	0.82[EUR][1000 genomes]
rs6700673	0.96[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs7415820	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7513716	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7544663	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554345	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7554916	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs902289	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs910697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429486	0.86[CEU][hapmap]
rs954679	0.81[JPT][hapmap]

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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1006298	ST7L	cis	Adipose Subcutaneous	GTEx
rs1006298	ST7L	cis	multi-tissue	Pritchard
rs1006298	ST7L	cis	lung	GTEx
rs1006298	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs1006298	ST7L	cis	Nerve Tibial	GTEx
rs1006298	ST7L	cis	lesional skin	skin_eQTL
rs1006298	ST7L	cis	Heart Left Ventricle	GTEx
rs1006298	ST7L	cis	Esophagus Muscularis	GTEx
rs1006298	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs1006298	ST7L	cis	Stomach	GTEx
rs1006298	ST7L	cis	Lymphoblastoid	GTEx
rs1006298	ST7L	cis	Thyroid	GTEx
rs1006298	ST7L	cis	uninvolved skin	skin_eQTL
rs1006298	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	chr1:113052000-113082600	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	chr1:113058800-113062600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:113058800-113062800	Weak transcription	NHDF-Ad	bronchial
28	chr1:113058800-113064800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:113058800-113067200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:113058800-113119400	Weak transcription	HepG2	liver
31	chr1:113059000-113062200	Weak transcription	Osteobl	bone
32	chr1:113059000-113062800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:113059000-113064800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:113059000-113064800	Weak transcription	NHLF	lung
35	chr1:113059000-113065200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:113059000-113067000	Weak transcription	Right Ventricle	heart
37	chr1:113059200-113062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:113059200-113067600	Weak transcription	Primary T cells from cord blood	blood
39	chr1:113059200-113071600	Weak transcription	Hela-S3	cervix
40	chr1:113059600-113069600	Weak transcription	Spleen	Spleen
41	chr1:113060000-113065200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:113060200-113062800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:113060200-113062800	Weak transcription	Ovary	ovary
44	chr1:113060200-113062800	Weak transcription	Right Atrium	heart
45	chr1:113060200-113064800	Weak transcription	Lung	lung
46	chr1:113060200-113065000	Weak transcription	Fetal Intestine Small	intestine
47	chr1:113060200-113067000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:113060200-113067000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:113060200-113067200	Weak transcription	Gastric	stomach
50	chr1:113060200-113069600	Weak transcription	Aorta	Aorta

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