Variant report

Variant	rs12054682
Chromosome Location	chr5:36229452-36229453
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	chr5:36220234..36224903-chr5:36227628..36232004,4	K562	blood:
2	chr5:36220506..36223464-chr5:36227618..36229963,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245711	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10461961	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10461962	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10461964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10461965	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10512642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10512648	1.00[AFR][1000 genomes]
rs10941282	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10941283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10941284	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12054662	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12054958	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12055219	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12652746	1.00[AFR][1000 genomes]
rs12654720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12655033	1.00[AFR][1000 genomes]
rs12656102	0.87[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12657110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12658779	0.87[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1364013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1364014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1364015	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16902793	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16902797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16902801	1.00[AFR][1000 genomes]
rs16902812	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16902813	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16902827	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16902836	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16902845	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16902871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16902911	0.86[CHB][hapmap];1.00[AMR][1000 genomes]
rs28362652	1.00[AFR][1000 genomes]
rs2937535	1.00[AFR][1000 genomes]
rs3849785	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3849787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3900936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4869470	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4869471	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4869472	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4869624	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4869627	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4869628	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4869629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4869630	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4869633	0.86[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4869637	0.87[CHB][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs56815690	0.84[ASN][1000 genomes]
rs59754678	0.82[ASN][1000 genomes]
rs6886540	0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs6898451	0.82[ASN][1000 genomes]
rs73081933	0.84[ASN][1000 genomes]
rs878608	0.87[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9637790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs991033	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs991034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830262	chr5:36074311-36293872	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	63 gene(s)	inside rSNPs	diseases
2	nsv1015638	chr5:36203646-36312576	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36179000-36230000	Weak transcription	Psoas Muscle	Psoas
2	chr5:36191800-36230000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:36196600-36236600	Weak transcription	GM12878-XiMat	blood
4	chr5:36198000-36238400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:36200000-36229600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:36200200-36239400	Weak transcription	Fetal Brain Male	brain
7	chr5:36201200-36230200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:36201400-36240000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:36213200-36230200	Weak transcription	Brain Germinal Matrix	brain
10	chr5:36213200-36237000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:36215200-36236600	Weak transcription	Small Intestine	intestine
12	chr5:36215800-36237800	Weak transcription	HMEC	breast
13	chr5:36219600-36230000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:36221000-36230200	Weak transcription	K562	blood
15	chr5:36221200-36230000	Weak transcription	HSMMtube	muscle
16	chr5:36221200-36230400	Weak transcription	Lung	lung
17	chr5:36221200-36238800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:36221400-36229600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:36221600-36230000	Weak transcription	Pancreas	Pancrea
20	chr5:36221600-36230200	Weak transcription	Gastric	stomach
21	chr5:36221600-36232600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:36221600-36235600	Weak transcription	Fetal Kidney	kidney
23	chr5:36221600-36236200	Weak transcription	Fetal Intestine Small	intestine
24	chr5:36221600-36238600	Weak transcription	Fetal Stomach	stomach
25	chr5:36221600-36239800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr5:36223000-36230600	Weak transcription	Brain Hippocampus Middle	brain
27	chr5:36224200-36229800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr5:36225200-36230400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:36225200-36230400	Weak transcription	Brain Substantia Nigra	brain
30	chr5:36225200-36237800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:36225400-36230400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:36225400-36237800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:36225400-36237800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:36225600-36229600	Weak transcription	Ovary	ovary
35	chr5:36225600-36230000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:36225600-36230400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:36225600-36239800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr5:36225800-36230000	Weak transcription	Aorta	Aorta
39	chr5:36225800-36230200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:36225800-36230200	Weak transcription	Left Ventricle	heart
41	chr5:36225800-36237800	Weak transcription	Fetal Lung	lung
42	chr5:36226000-36230200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:36226000-36230200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:36226000-36233000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:36226000-36236600	Weak transcription	Fetal Intestine Large	intestine
46	chr5:36226000-36237000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr5:36226000-36237200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr5:36226000-36239800	Weak transcription	Fetal Brain Female	brain
49	chr5:36226000-36240400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:36226000-36240400	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links