Variant report

Variant	rs12086559
Chromosome Location	chr1:180851627-180851628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180850782..180851739-chr1:181135389..181136343,4	K562	blood:
2	chr1:180846972..180853051-chr1:181055773..181063614,10	MCF-7	breast:
3	chr1:180850817..180851784-chr1:181135445..181136674,4	MCF-7	breast:
4	chr1:180850757..180851768-chr1:180886019..180887077,4	MCF-7	breast:
5	chr1:180851211..180851748-chr1:180886156..180886674,2	MCF-7	breast:
6	chr1:180850662..180852317-chr1:180933020..180935917,2	K562	blood:
7	chr1:180851368..180853381-chr1:180991093..180993402,2	MCF-7	breast:
8	chr1:180850742..180851768-chr1:181111240..181112026,6	MCF-7	breast:
9	chr1:180850805..180851714-chr1:181393724..181394349,2	MCF-7	breast:
10	chr1:180849796..180851972-chr1:181110307..181113193,2	MCF-7	breast:
11	chr1:180848547..180852061-chr1:181053599..181056742,3	MCF-7	breast:
12	chr1:180850269..180851818-chr1:181135334..181136683,10	MCF-7	breast:
13	chr1:180850812..180851717-chr1:181007258..181008144,2	K562	blood:
14	chr1:180849811..180851965-chr1:181072778..181074539,2	MCF-7	breast:
15	chr1:180832480..180833036-chr1:180850771..180851656,2	K562	blood:
16	chr1:180747652..180748487-chr1:180851159..180851718,2	MCF-7	breast:
17	chr1:180849682..180853088-chr1:181056991..181059628,4	K562	blood:
18	chr1:180844696..180847616-chr1:180851368..180852915,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA1614-4	chr1:180850898-180852385	refGeneNc_676_NR_036490

No data

Variant related genes	Relation type
ENSG00000135823	Chromatin interaction
ENSG00000272198	Chromatin interaction
ENSG00000251520	Chromatin interaction
ENSG00000162783	Chromatin interaction
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10914085	0.84[YRI][hapmap]
rs10914125	0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12059644	0.82[YRI][hapmap]
rs12063893	0.81[YRI][hapmap]
rs12068624	0.84[YRI][hapmap]
rs12071498	0.81[YRI][hapmap]
rs12073086	0.86[YRI][hapmap]
rs12079208	0.81[YRI][hapmap]
rs12088182	0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12088419	0.87[YRI][hapmap]
rs12088425	0.82[YRI][hapmap]
rs12089778	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12090251	0.82[YRI][hapmap]
rs12091686	0.83[YRI][hapmap]
rs12092920	0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12095486	0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12095684	0.81[YRI][hapmap]
rs12096475	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58065433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59562665	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6659121	0.83[YRI][hapmap]
rs6676373	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6682537	0.84[YRI][hapmap]
rs6691204	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73047730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73047732	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73047734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73047747	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73047748	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats 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 target site	97 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180773800-180853200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:180805800-180881000	Weak transcription	Aorta	Aorta
3	chr1:180812200-180867000	Weak transcription	Ovary	ovary
4	chr1:180822000-180862800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:180822800-180862800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:180823000-180854600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:180823600-180860000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:180823800-180862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:180824000-180867600	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:180824000-180880800	Weak transcription	Right Ventricle	heart
11	chr1:180827800-180856600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:180828000-180852400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:180828000-180853200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:180828000-180853200	Weak transcription	NHEK	skin
15	chr1:180828600-180867800	Weak transcription	HSMM	muscle
16	chr1:180830000-180867600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:180831200-180858600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:180831600-180852600	Weak transcription	Fetal Lung	lung
19	chr1:180832400-180853200	Weak transcription	Fetal Stomach	stomach
20	chr1:180832600-180854400	Weak transcription	Liver	Liver
21	chr1:180832800-180861800	Weak transcription	HepG2	liver
22	chr1:180834800-180855800	Weak transcription	Gastric	stomach
23	chr1:180835400-180862800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:180835600-180855400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:180835800-180856600	Weak transcription	Fetal Intestine Large	intestine
26	chr1:180835800-180858800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:180835800-180861600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:180835800-180870400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:180841000-180867800	Weak transcription	Lung	lung
30	chr1:180841800-180855000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:180841800-180856000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:180842200-180857200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:180842200-180857600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:180842200-180858600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:180842400-180858000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:180843400-180853200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:180843600-180855800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:180843600-180856800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:180843600-180862800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:180843800-180858000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:180843800-180858600	Weak transcription	HMEC	breast
42	chr1:180844200-180872200	Weak transcription	Esophagus	oesophagus
43	chr1:180844400-180853800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:180844400-180856000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:180844400-180858000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:180844400-180867400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:180845800-180856400	Weak transcription	Psoas Muscle	Psoas
48	chr1:180845800-180869000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:180847200-180852400	Weak transcription	Adipose Nuclei	Adipose
50	chr1:180847400-180875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links