Variant report

Variant	rs2289478
Chromosome Location	chr1:9990112-9990113
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9988737..9991346-chr1:10009208..10011504,2	K562	blood:
2	chr1:9970332..9972521-chr1:9989080..9990638,2	K562	blood:
3	chr1:9970332..9972521-chr1:9987991..9990638,3	K562	blood:
4	chr1:9950543..9952376-chr1:9989570..9991778,2	K562	blood:
5	chr1:9979666..9982180-chr1:9989888..9991989,2	K562	blood:

Variant related genes	Relation type
ENSG00000178585	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11121501	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11121509	0.93[AMR][1000 genomes]
rs12058979	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12059092	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12060375	0.88[AMR][1000 genomes]
rs12062953	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12064822	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12065908	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070725	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12071307	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12082318	0.93[AMR][1000 genomes]
rs12086598	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12088598	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094254	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097182	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034440	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297843	0.95[AMR][1000 genomes]
rs4845912	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846104	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846108	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57702810	0.87[ASN][1000 genomes]
rs60132751	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61743470	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6663059	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664208	0.88[AMR][1000 genomes]
rs7516611	0.91[AMR][1000 genomes]
rs7535945	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	nsv534854	chr1:9964726-10001012	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
rs2289478	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9971400-9993600	Weak transcription	Aorta	Aorta
2	chr1:9971400-10002000	Weak transcription	Small Intestine	intestine
3	chr1:9971600-9991200	Weak transcription	NHEK	skin
4	chr1:9971800-9991800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:9972600-10002200	Weak transcription	Right Atrium	heart
6	chr1:9975200-10002600	Weak transcription	Stomach Mucosa	stomach
7	chr1:9977000-9991800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:9978200-9990200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:9980400-9990200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:9983200-10002200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:9983200-10002400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:9983600-10002400	Weak transcription	Fetal Heart	heart
13	chr1:9983600-10002400	Weak transcription	Right Ventricle	heart
14	chr1:9984000-10002200	Weak transcription	HMEC	breast
15	chr1:9984600-9996400	Weak transcription	NHDF-Ad	bronchial
16	chr1:9984600-10002600	Weak transcription	Esophagus	oesophagus
17	chr1:9985200-9996200	Weak transcription	Hela-S3	cervix
18	chr1:9985800-9996200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:9986000-9992000	Weak transcription	Gastric	stomach
20	chr1:9986600-9996800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:9986800-9991400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:9986800-10000200	Strong transcription	Primary T cells from cord blood	blood
23	chr1:9987000-9992400	Strong transcription	Fetal Brain Female	brain
24	chr1:9987000-9993600	Weak transcription	Fetal Kidney	kidney
25	chr1:9987000-9996800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:9987000-10002200	Weak transcription	Fetal Brain Male	brain
27	chr1:9987200-9997200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:9987200-10002200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:9987400-9991800	Strong transcription	Fetal Intestine Small	intestine
30	chr1:9987400-10000400	Strong transcription	Fetal Stomach	stomach
31	chr1:9987400-10002000	Weak transcription	Colonic Mucosa	Colon
32	chr1:9987600-9995600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:9987600-9999400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:9987800-9991600	Strong transcription	Fetal Intestine Large	intestine
35	chr1:9987800-9996400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:9987800-9996600	Strong transcription	Adipose Nuclei	Adipose
37	chr1:9987800-9996600	Strong transcription	Liver	Liver
38	chr1:9987800-10002200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:9988000-9990200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:9988000-9992200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:9988000-9996600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:9988000-9998600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr1:9988000-10002000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:9988200-9991400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:9988200-9994800	Weak transcription	Psoas Muscle	Psoas
46	chr1:9988200-9996600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr1:9988200-10002400	Weak transcription	NHLF	lung
48	chr1:9988400-9990600	Strong transcription	Primary B cells from cord blood	blood
49	chr1:9988400-9990600	Strong transcription	Fetal Lung	lung
50	chr1:9988400-9990600	Strong transcription	Dnd41	blood

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