Variant report

Variant	rs1220422
Chromosome Location	chr1:10004882-10004883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10004867-10005406	HepG2	liver:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10002125..10006916-chr1:10090169..10095056,10	K562	blood:
2	chr1:10001502..10006445-chr1:10090966..10096976,9	MCF-7	breast:
3	chr1:9969188..9972816-chr1:10001560..10005397,4	MCF-7	breast:
4	chr1:10002086..10005062-chr1:10091281..10093134,5	K562	blood:
5	chr1:10002061..10004916-chr1:10091716..10094596,6	MCF-7	breast:
6	chr1:9969022..9974825-chr1:10002123..10006220,12	K562	blood:
7	chr1:9968043..9973723-chr1:10001891..10008599,10	K562	blood:
8	chr1:10001294..10005828-chr1:10093316..10096471,4	K562	blood:
9	chr1:10003032..10004962-chr1:10118663..10120416,2	MCF-7	breast:
10	chr1:9881807..9884566-chr1:10002290..10004897,3	K562	blood:
11	chr1:9969199..9972073-chr1:10003014..10005092,3	MCF-7	breast:
12	chr1:9881807..9884566-chr1:10002965..10004897,2	K562	blood:
13	chr1:9946281..9947867-chr1:10004858..10007220,2	K562	blood:

No data

Variant related genes	Relation type
LZIC	TF binding region
RN7SKP269	TF binding region
ENSG00000130939	Chromatin interaction
ENSG00000171603	Chromatin interaction
ENSG00000233623	Chromatin interaction
ENSG00000178585	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10779735	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11121508	0.93[AFR][1000 genomes]
rs12026401	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128632	0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12128636	0.87[AFR][1000 genomes]
rs1220398	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1237370	0.93[AFR][1000 genomes]
rs12744387	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2380188	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3013785	0.87[AFR][1000 genomes]
rs4073852	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41280780	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782860	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61785621	0.95[AFR][1000 genomes]
rs6541074	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663108	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6673580	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683452	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72859517	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522568	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534615	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943169	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	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
9	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
10	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
11	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
rs1220422	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10004000-10005200	Enhancers	Spleen	Spleen
2	chr1:10004000-10010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:10004000-10010600	Weak transcription	Fetal Heart	heart
4	chr1:10004000-10034000	Weak transcription	Aorta	Aorta
5	chr1:10004200-10005000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr1:10004200-10005200	Enhancers	Adipose Nuclei	Adipose
7	chr1:10004200-10005200	Enhancers	Fetal Muscle Leg	muscle
8	chr1:10004200-10007000	Weak transcription	Fetal Stomach	stomach
9	chr1:10004200-10007200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:10004200-10010000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:10004200-10010400	Weak transcription	Fetal Lung	lung
12	chr1:10004200-10010600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:10004200-10010600	Weak transcription	Fetal Brain Male	brain
14	chr1:10004200-10010600	Weak transcription	Fetal Kidney	kidney
15	chr1:10004200-10010600	Weak transcription	Ovary	ovary
16	chr1:10004200-10011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:10004200-10019400	Weak transcription	NH-A	brain
18	chr1:10004200-10021000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:10004200-10033800	Weak transcription	Gastric	stomach
20	chr1:10004400-10005000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr1:10004400-10005000	Enhancers	Stomach Smooth Muscle	stomach
22	chr1:10004400-10005200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:10004400-10005400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:10004400-10007200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:10004400-10007400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:10004400-10009200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:10004400-10010000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:10004400-10010000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:10004400-10010000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:10004400-10010000	Weak transcription	Stomach Mucosa	stomach
31	chr1:10004400-10010200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:10004400-10010200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:10004400-10010200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:10004400-10010200	Weak transcription	Placenta	Placenta
35	chr1:10004400-10010400	Weak transcription	Esophagus	oesophagus
36	chr1:10004400-10010600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:10004400-10010600	Weak transcription	Brain Angular Gyrus	brain
38	chr1:10004400-10010600	Weak transcription	Fetal Brain Female	brain
39	chr1:10004400-10010600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:10004400-10010800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:10004400-10018200	Weak transcription	NHLF	lung
42	chr1:10004400-10021200	Weak transcription	HSMM	muscle
43	chr1:10004400-10031600	Weak transcription	Fetal Intestine Large	intestine
44	chr1:10004600-10005000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:10004600-10005000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:10004600-10005000	Flanking Active TSS	HepG2	liver
47	chr1:10004600-10005200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr1:10004600-10007000	Weak transcription	Primary B cells from cord blood	blood
49	chr1:10004600-10007200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:10004600-10007400	Weak transcription	Primary hematopoietic stem cells	blood

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