Variant report

Variant	rs12060280
Chromosome Location	chr1:180643930-180643931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180600246..180602406-chr1:180641858..180644833,2	K562	blood:

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10914059	1.00[YRI][hapmap]
rs10914060	1.00[YRI][hapmap]
rs10914092	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10914097	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10914099	1.00[AMR][1000 genomes]
rs10914100	1.00[AMR][1000 genomes]
rs12058670	1.00[AMR][1000 genomes]
rs12059839	1.00[AMR][1000 genomes]
rs12062543	1.00[AMR][1000 genomes]
rs12062549	1.00[AMR][1000 genomes]
rs12064761	1.00[AMR][1000 genomes]
rs12068825	1.00[AMR][1000 genomes]
rs12070554	1.00[AMR][1000 genomes]
rs12073278	1.00[AMR][1000 genomes]
rs12076029	1.00[AMR][1000 genomes]
rs12076333	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12076671	1.00[AMR][1000 genomes]
rs12079458	1.00[YRI][hapmap]
rs12082348	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12083109	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12084365	1.00[YRI][hapmap]
rs12084562	1.00[AMR][1000 genomes]
rs12085100	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12087750	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12089474	1.00[AMR][1000 genomes]
rs12089522	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12089583	1.00[AMR][1000 genomes]
rs12089730	1.00[AMR][1000 genomes]
rs12090598	1.00[AMR][1000 genomes]
rs12092799	1.00[AMR][1000 genomes]
rs12093933	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12095275	1.00[AMR][1000 genomes]
rs12095957	1.00[AMR][1000 genomes]
rs12097202	1.00[AMR][1000 genomes]
rs57004467	1.00[AMR][1000 genomes]
rs59193426	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv947336	chr1:180642298-180656857	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180602000-180645200	Weak transcription	Gastric	stomach
2	chr1:180631600-180644400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:180632200-180644800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:180633200-180672000	Weak transcription	K562	blood
5	chr1:180635000-180644800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:180635200-180654800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:180636400-180647200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:180636400-180651800	Weak transcription	Ovary	ovary
9	chr1:180640200-180662200	Weak transcription	Fetal Heart	heart
10	chr1:180640600-180660600	Weak transcription	Right Ventricle	heart
11	chr1:180641000-180653200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:180641200-180644000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:180641200-180644400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:180641200-180647400	Weak transcription	Fetal Intestine Small	intestine
15	chr1:180641200-180653400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:180641200-180662800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:180641400-180644800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:180641600-180661200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:180641800-180644800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:180642200-180658200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:180642400-180644600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:180642600-180644000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:180642800-180644800	Weak transcription	Aorta	Aorta
24	chr1:180642800-180644800	Weak transcription	Small Intestine	intestine
25	chr1:180642800-180646200	Weak transcription	Pancreas	Pancrea
26	chr1:180643000-180644400	Weak transcription	A549	lung
27	chr1:180643000-180651400	Weak transcription	Primary B cells from cord blood	blood
28	chr1:180643000-180659000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:180643200-180647200	Weak transcription	Primary T cells from cord blood	blood
30	chr1:180643400-180644000	Genic enhancers	Left Ventricle	heart
31	chr1:180643800-180644000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:180643800-180644000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr1:180643800-180644200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:180643800-180645000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr1:180643800-180645000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:180643800-180645200	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr1:180643800-180645200	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links