Variant report

Variant	rs10779734
Chromosome Location	chr1:10041977-10041978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11121510	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11121512	0.87[ASN][1000 genomes]
rs11828	0.85[ASN][1000 genomes]
rs12140009	0.83[ASN][1000 genomes]
rs12140015	0.83[ASN][1000 genomes]
rs12140058	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1220389	0.81[ASN][1000 genomes]
rs1220399	0.85[ASN][1000 genomes]
rs1220400	0.83[ASN][1000 genomes]
rs1220402	0.88[ASN][1000 genomes]
rs1220420	0.88[ASN][1000 genomes]
rs1220421	0.88[ASN][1000 genomes]
rs1220424	0.87[ASN][1000 genomes]
rs1234694	0.87[ASN][1000 genomes]
rs1628143	0.83[ASN][1000 genomes]
rs1660733	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2890358	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3003377	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3003378	0.86[ASN][1000 genomes]
rs3013784	0.85[ASN][1000 genomes]
rs3123522	0.80[ASN][1000 genomes]
rs6541073	0.89[ASN][1000 genomes]
rs6661806	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6664631	0.88[ASN][1000 genomes]
rs6678023	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6680076	0.81[ASN][1000 genomes]
rs7517360	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7517806	0.80[ASN][1000 genomes]
rs7517812	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7539191	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10779734	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10011000-10044800	Weak transcription	NHDF-Ad	bronchial
2	chr1:10011800-10042200	Weak transcription	K562	blood
3	chr1:10016400-10042400	Weak transcription	HMEC	breast
4	chr1:10021400-10043200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:10021600-10049000	Weak transcription	HSMM	muscle
6	chr1:10023400-10044000	Weak transcription	HepG2	liver
7	chr1:10025800-10046800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:10028400-10050000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:10029600-10042200	Weak transcription	GM12878-XiMat	blood
10	chr1:10030400-10043000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:10030800-10044600	Weak transcription	Brain Germinal Matrix	brain
12	chr1:10031200-10042200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:10031200-10042200	Weak transcription	Small Intestine	intestine
14	chr1:10031600-10044600	Strong transcription	Fetal Intestine Large	intestine
15	chr1:10031600-10045600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:10031600-10046200	Strong transcription	Fetal Intestine Small	intestine
17	chr1:10031600-10047200	Strong transcription	Fetal Stomach	stomach
18	chr1:10032000-10043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:10032000-10045200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:10032000-10046600	Strong transcription	Liver	Liver
21	chr1:10032200-10044200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:10032200-10044200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:10032200-10045400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:10032400-10042200	Weak transcription	NH-A	brain
25	chr1:10032400-10044200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:10032600-10043400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:10032600-10044400	Strong transcription	Primary T cells from cord blood	blood
28	chr1:10032800-10057000	Weak transcription	Psoas Muscle	Psoas
29	chr1:10033800-10044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:10034200-10042200	Weak transcription	Dnd41	blood
31	chr1:10034400-10042800	Strong transcription	Placenta	Placenta
32	chr1:10034400-10048000	Weak transcription	Stomach Mucosa	stomach
33	chr1:10034600-10042200	Weak transcription	Aorta	Aorta
34	chr1:10034800-10042800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:10035600-10051800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:10036000-10042200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:10036000-10044600	Weak transcription	Fetal Kidney	kidney
38	chr1:10036000-10050400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:10036200-10042200	Weak transcription	NHLF	lung
40	chr1:10036200-10042400	Weak transcription	Brain Substantia Nigra	brain
41	chr1:10036600-10042000	Weak transcription	Pancreas	Pancrea
42	chr1:10036600-10043800	Weak transcription	Brain Angular Gyrus	brain
43	chr1:10036600-10044800	Weak transcription	Fetal Heart	heart
44	chr1:10036600-10047800	Weak transcription	NHEK	skin
45	chr1:10036800-10042000	Weak transcription	Esophagus	oesophagus
46	chr1:10036800-10051200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:10037000-10042200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:10037200-10054600	Weak transcription	Fetal Brain Female	brain
49	chr1:10037600-10042800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:10037800-10044200	Strong transcription	Left Ventricle	heart

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