Variant report

Variant	rs41280780
Chromosome Location	chr1:10010344-10010345
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10008573..10013502-chr1:10090291..10096219,9	MCF-7	breast:
2	chr1:10010235..10011004-chr1:10092319..10093175,4	MCF-7	breast:
3	chr1:10009350..10011460-chr1:10068351..10069869,2	K562	blood:
4	chr1:10010111..10010962-chr1:10092219..10093003,3	MCF-7	breast:
5	chr1:10006856..10008883-chr1:10008961..10010620,2	K562	blood:
6	chr1:10009323..10011578-chr1:10096303..10099000,2	MCF-7	breast:
7	chr1:10008967..10010504-chr1:10091583..10094511,2	MCF-7	breast:
8	chr1:9988737..9991346-chr1:10009208..10011504,2	K562	blood:
9	chr1:10009468..10012009-chr1:10018654..10021337,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000202415	Chromatin interaction
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10779735	0.85[ASN][1000 genomes]
rs12026401	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128632	0.83[ASN][1000 genomes]
rs1220422	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744387	0.88[ASN][1000 genomes]
rs2380188	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34851031	0.84[AMR][1000 genomes]
rs4073852	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61782860	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541074	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673580	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683452	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72859517	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522568	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534615	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943169	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41280780	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10004000-10010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:10004000-10010600	Weak transcription	Fetal Heart	heart
3	chr1:10004000-10034000	Weak transcription	Aorta	Aorta
4	chr1:10004200-10010400	Weak transcription	Fetal Lung	lung
5	chr1:10004200-10010600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:10004200-10010600	Weak transcription	Fetal Brain Male	brain
7	chr1:10004200-10010600	Weak transcription	Fetal Kidney	kidney
8	chr1:10004200-10010600	Weak transcription	Ovary	ovary
9	chr1:10004200-10011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:10004200-10019400	Weak transcription	NH-A	brain
11	chr1:10004200-10021000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:10004200-10033800	Weak transcription	Gastric	stomach
13	chr1:10004400-10010400	Weak transcription	Esophagus	oesophagus
14	chr1:10004400-10010600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:10004400-10010600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:10004400-10010600	Weak transcription	Fetal Brain Female	brain
17	chr1:10004400-10010600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:10004400-10010800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:10004400-10018200	Weak transcription	NHLF	lung
20	chr1:10004400-10021200	Weak transcription	HSMM	muscle
21	chr1:10004400-10031600	Weak transcription	Fetal Intestine Large	intestine
22	chr1:10004600-10010400	Weak transcription	Primary T cells from cord blood	blood
23	chr1:10004600-10010400	Weak transcription	Thymus	Thymus
24	chr1:10004600-10010600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:10004600-10010600	Weak transcription	NHDF-Ad	bronchial
26	chr1:10004600-10010600	Weak transcription	Osteobl	bone
27	chr1:10004600-10021000	Weak transcription	HSMMtube	muscle
28	chr1:10004600-10032400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:10004800-10010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:10004800-10010600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:10004800-10010600	Weak transcription	Right Ventricle	heart
32	chr1:10004800-10010600	Weak transcription	Dnd41	blood
33	chr1:10004800-10010600	Weak transcription	Hela-S3	cervix
34	chr1:10004800-10010600	Weak transcription	NHEK	skin
35	chr1:10004800-10031600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:10004800-10032200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:10004800-10032400	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:10005600-10015000	Strong transcription	Fetal Intestine Small	intestine
39	chr1:10006000-10010400	Weak transcription	HepG2	liver
40	chr1:10007000-10010600	Weak transcription	Psoas Muscle	Psoas
41	chr1:10008000-10010400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:10008000-10010400	Weak transcription	Pancreas	Pancrea
43	chr1:10008000-10010600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:10008000-10010600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:10008000-10010600	Weak transcription	K562	blood
46	chr1:10008000-10014200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:10008000-10031800	Weak transcription	Lung	lung
48	chr1:10008000-10032000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:10008000-10032200	Weak transcription	Colonic Mucosa	Colon
50	chr1:10008000-10035000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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