Variant report

Variant	rs12030554
Chromosome Location	chr1:185087634-185087635
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185086646..185088297-chr1:185088839..185091259,2	K562	blood:
2	chr1:185085659..185087885-chr1:185092859..185095086,2	K562	blood:
3	chr1:185087227..185089140-chr1:185125216..185126915,2	MCF-7	breast:
4	chr1:185079216..185081191-chr1:185086441..185087955,2	K562	blood:

Variant related genes	Relation type
ENSG00000116668	Chromatin interaction
ENSG00000121486	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1046592	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10489580	0.81[JPT][hapmap]
rs10737256	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10752945	0.84[ASN][1000 genomes]
rs10797998	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs10797999	0.84[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs10911678	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10911680	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11588646	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12025737	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12081098	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12086086	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs12404644	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs12566975	0.87[ASN][1000 genomes]
rs1322646	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1407555	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1407556	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1407557	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1544052	0.83[CHB][hapmap]
rs1884447	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2057222	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2146329	0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs3753569	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4549995	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6424971	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6700484	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7519019	0.81[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7547420	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv521613	chr1:185071831-185171869	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv872588	chr1:185081903-185117688	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185018400-185101800	Weak transcription	Fetal Brain Male	brain
2	chr1:185054400-185101800	Weak transcription	A549	lung
3	chr1:185055400-185096200	Weak transcription	Hela-S3	cervix
4	chr1:185056200-185124200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:185057600-185094600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:185058600-185089000	Weak transcription	Ovary	ovary
7	chr1:185058800-185093600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:185059000-185124800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:185065800-185088600	Weak transcription	NHDF-Ad	bronchial
10	chr1:185067800-185095400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:185068400-185110200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:185069400-185091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:185069600-185088200	Weak transcription	Fetal Lung	lung
14	chr1:185070000-185101400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:185070200-185088800	Weak transcription	HSMM	muscle
16	chr1:185070400-185089200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:185073600-185088200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:185073600-185092800	Weak transcription	Fetal Kidney	kidney
19	chr1:185073600-185115000	Weak transcription	NH-A	brain
20	chr1:185073800-185088600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:185073800-185088600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:185074000-185088600	Weak transcription	NHLF	lung
23	chr1:185077400-185088200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:185078800-185088800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:185078800-185102000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:185079800-185102000	Weak transcription	Small Intestine	intestine
27	chr1:185080000-185101000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:185081200-185091400	Weak transcription	GM12878-XiMat	blood
29	chr1:185081600-185091000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:185081800-185088600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:185081800-185088800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:185081800-185092800	Weak transcription	HUVEC	blood vessel
33	chr1:185082000-185088600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:185082000-185092800	Weak transcription	K562	blood
35	chr1:185082200-185088600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:185082200-185095200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:185082400-185088800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:185082400-185093600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:185082600-185088200	Weak transcription	Brain Substantia Nigra	brain
40	chr1:185082600-185100400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:185082600-185101400	Weak transcription	Esophagus	oesophagus
42	chr1:185082600-185125400	Weak transcription	Spleen	Spleen
43	chr1:185082800-185088200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:185083400-185093400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:185084000-185089200	Weak transcription	Left Ventricle	heart
46	chr1:185084200-185088200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:185084200-185089000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:185084200-185103400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:185084200-185124400	Weak transcription	Right Ventricle	heart
50	chr1:185084400-185091000	Weak transcription	Brain Angular Gyrus	brain

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