Variant report

Variant	rs1220402
Chromosome Location	chr1:9999539-9999540
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:9999005-10000505	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:9998139-9999736	K562	blood:	n/a	n/a
3	POLR2A	chr1:9999454-9999593	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:9969786..9972785-chr1:9998354..10000528,2	K562	blood:
2	chr1:9979462..9981194-chr1:9999339..10001219,2	K562	blood:
3	chr1:9923513..9926464-chr1:9996887..9999846,2	K562	blood:
4	chr1:9998207..10001225-chr1:10001288..10004124,5	MCF-7	breast:

Variant related genes	Relation type
LZIC	TF binding region
ENSG00000228150	TF binding region
NMNAT1	TF binding region
ENSG00000162441	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000178585	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10779734	0.88[ASN][1000 genomes]
rs11121510	0.87[ASN][1000 genomes]
rs11121512	0.84[ASN][1000 genomes]
rs11828	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12140009	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140015	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140058	0.89[ASN][1000 genomes]
rs1220389	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1220397	0.83[ASN][1000 genomes]
rs1220399	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1220400	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1220420	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1220421	0.93[ASN][1000 genomes]
rs1220424	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1234694	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1237370	0.84[ASN][1000 genomes]
rs1628143	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1660733	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2890358	0.91[ASN][1000 genomes]
rs2919694	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3003377	0.83[ASN][1000 genomes]
rs3003378	0.84[ASN][1000 genomes]
rs3013783	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3013784	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6541073	0.91[ASN][1000 genomes]
rs6661806	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6664631	0.86[ASN][1000 genomes]
rs6678023	0.86[ASN][1000 genomes]
rs7517360	0.88[ASN][1000 genomes]
rs7517812	0.84[ASN][1000 genomes]
rs7539191	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
12	nsv947175	chr1:9996275-10009860	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1220402	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9971400-10002000	Weak transcription	Small Intestine	intestine
2	chr1:9972600-10002200	Weak transcription	Right Atrium	heart
3	chr1:9975200-10002600	Weak transcription	Stomach Mucosa	stomach
4	chr1:9983200-10002200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:9983200-10002400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:9983600-10002400	Weak transcription	Fetal Heart	heart
7	chr1:9983600-10002400	Weak transcription	Right Ventricle	heart
8	chr1:9984000-10002200	Weak transcription	HMEC	breast
9	chr1:9984600-10002600	Weak transcription	Esophagus	oesophagus
10	chr1:9986800-10000200	Strong transcription	Primary T cells from cord blood	blood
11	chr1:9987000-10002200	Weak transcription	Fetal Brain Male	brain
12	chr1:9987200-10002200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:9987400-10000400	Strong transcription	Fetal Stomach	stomach
14	chr1:9987400-10002000	Weak transcription	Colonic Mucosa	Colon
15	chr1:9987800-10002200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:9988000-10002000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:9988200-10002400	Weak transcription	NHLF	lung
18	chr1:9988400-10000200	Strong transcription	Fetal Muscle Leg	muscle
19	chr1:9988400-10001600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:9988400-10002000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:9988400-10002200	Weak transcription	HUVEC	blood vessel
22	chr1:9989600-10002200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:9990200-10002400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:9990200-10002400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:9990600-10002200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:9990600-10002400	Weak transcription	HSMMtube	muscle
27	chr1:9992200-10002000	Strong transcription	Fetal Intestine Small	intestine
28	chr1:9992200-10002200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:9992200-10002400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:9992200-10002400	Weak transcription	Osteobl	bone
31	chr1:9992400-10002200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:9992400-10002400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:9992400-10002600	Weak transcription	Pancreas	Pancrea
34	chr1:9992600-10000000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:9992600-10002600	Weak transcription	Lung	lung
36	chr1:9992800-10002600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:9993400-10000000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:9994200-10002600	Weak transcription	Gastric	stomach
39	chr1:9994400-10002600	Weak transcription	Aorta	Aorta
40	chr1:9994600-10002000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:9994600-10002400	Weak transcription	Ovary	ovary
42	chr1:9995200-9999600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:9995200-9999600	Weak transcription	HepG2	liver
44	chr1:9995200-10002200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:9995600-10002000	Weak transcription	Psoas Muscle	Psoas
46	chr1:9995600-10002600	Weak transcription	Spleen	Spleen
47	chr1:9995800-10002200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:9995800-10002200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:9995800-10002200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:9995800-10002400	Weak transcription	A549	lung

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