Variant report

Variant	rs10745330
Chromosome Location	chr1:113083439-113083440
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113077855..113079726-chr1:113080031..113084166,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RHOC-3	chr1:113083401-113083494	NONHSAT005246

Extended variants
information (count: 50 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1001494	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1006298	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10776755	0.89[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs10776756	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10776757	0.89[CEU][hapmap]
rs10857963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102497	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102512	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11584092	0.88[CEU][hapmap]
rs12046208	0.89[CEU][hapmap];0.83[GIH][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap]
rs12126277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12728001	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994604	0.88[EUR][1000 genomes]
rs2932532	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs2932536	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs2999154	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs2999155	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs3013439	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs3013440	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs3103450	0.81[EUR][1000 genomes]
rs351372	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]
rs4838959	0.82[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap]
rs4839254	0.85[CEU][hapmap]
rs6537743	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537748	0.81[GIH][hapmap]
rs6537749	0.82[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs6666579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6669096	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6679414	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6682737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6691932	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6700673	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs7415820	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes]
rs7512948	0.81[EUR][1000 genomes]
rs7513716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522288	0.82[CEU][hapmap]
rs7524494	0.81[EUR][1000 genomes]
rs7544663	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];0.88[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546094	0.88[EUR][1000 genomes]
rs7554345	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7554916	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs902289	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap]
rs910697	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9429486	0.89[CEU][hapmap]
rs954679	0.81[JPT][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	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs10745330	ST7L	cis	lung	GTEx
rs10745330	ST7L	cis	lymphoblastoid	seeQTL
rs10745330	ALX3	cis	parietal	SCAN
rs10745330	ST7L	cis	uninvolved skin	skin_eQTL
rs10745330	ST7L	cis	Artery Tibial	GTEx
rs10745330	C1orf162	cis	parietal	SCAN
rs10745330	ST7L	cis	Stomach	GTEx
rs10745330	ST7L	cis	Nerve Tibial	GTEx
rs10745330	ST7L	cis	Heart Left Ventricle	GTEx
rs10745330	ST7L	cis	Thyroid	GTEx
rs10745330	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs10745330	ST7L	cis	normal skin	skin_eQTL
rs10745330	ST7L	cis	Adipose Subcutaneous	GTEx
rs10745330	ST7L	cis	Lymphoblastoid	GTEx
rs10745330	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs10745330	WNT2B	cis	parietal	SCAN
rs10745330	ST7L	cis	multi-tissue	Pritchard
rs10745330	ST7L	cis	lesional skin	skin_eQTL
rs10745330	ST7L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113052200-113093200	Weak transcription	Brain Substantia Nigra	brain
2	chr1:113055800-113085200	Weak transcription	Thymus	Thymus
3	chr1:113058400-113086600	Weak transcription	A549	lung
4	chr1:113058800-113119400	Weak transcription	HepG2	liver
5	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
6	chr1:113062400-113117400	Weak transcription	Psoas Muscle	Psoas
7	chr1:113063400-113092400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:113065000-113092400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:113065200-113114800	Weak transcription	Small Intestine	intestine
11	chr1:113065400-113114600	Weak transcription	Fetal Brain Male	brain
12	chr1:113065800-113086200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:113066000-113088800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:113066000-113114600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:113066200-113114400	Weak transcription	Dnd41	blood
17	chr1:113067000-113083800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:113067000-113117400	Weak transcription	Fetal Thymus	thymus
19	chr1:113067800-113083800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:113067800-113090200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:113068000-113089600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:113068000-113100200	Weak transcription	Fetal Heart	heart
23	chr1:113068600-113086400	Weak transcription	HUVEC	blood vessel
24	chr1:113068800-113087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:113070200-113083800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:113070400-113086000	Weak transcription	Spleen	Spleen
27	chr1:113070400-113095400	Weak transcription	Gastric	stomach
28	chr1:113070400-113120600	Weak transcription	Right Ventricle	heart
29	chr1:113070600-113088200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:113070600-113111600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:113070600-113112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:113070600-113112400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:113070600-113117800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:113070600-113120200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
36	chr1:113070800-113083800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:113071200-113090600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:113072000-113084400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:113072000-113114400	Weak transcription	Brain Anterior Caudate	brain
40	chr1:113072600-113087000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:113075200-113084000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:113076400-113115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:113078800-113090200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:113079400-113084800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:113079600-113087000	Weak transcription	HSMMtube	muscle
46	chr1:113080000-113084000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:113080000-113084600	Strong transcription	Liver	Liver
48	chr1:113080000-113085400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:113080200-113084600	Strong transcription	Primary T cells from cord blood	blood
50	chr1:113080200-113085800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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