Variant report

Variant	rs6488275
Chromosome Location	chr12:10379180-10379181
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	chr12:10363710..10369534-chr12:10376619..10381190,6	K562	blood:

Variant related genes	Relation type
ENSG00000255958	Chromatin interaction
ENSG00000139112	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10845104	0.87[CEU][hapmap]
rs11053722	0.82[CEU][hapmap];0.81[ASN][1000 genomes]
rs11830137	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304713	0.87[CEU][hapmap]
rs12311695	0.80[ASN][1000 genomes]
rs12315815	0.85[CEU][hapmap]
rs12321554	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12818742	0.84[EUR][1000 genomes]
rs12821332	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12824930	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12828163	0.82[EUR][1000 genomes]
rs12828540	0.85[CEU][hapmap]
rs12829898	0.87[CEU][hapmap]
rs12832221	0.82[CEU][hapmap]
rs17206564	0.87[CEU][hapmap]
rs2537793	0.87[CEU][hapmap]
rs2537805	0.82[EUR][1000 genomes]
rs2617128	0.87[CEU][hapmap]
rs2617135	0.87[CEU][hapmap];0.80[ASN][1000 genomes]
rs2617137	0.87[CEU][hapmap];0.81[ASN][1000 genomes]
rs2927558	0.81[ASN][1000 genomes]
rs35510688	0.82[EUR][1000 genomes]
rs35567183	0.87[EUR][1000 genomes]
rs4346056	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs4365134	0.84[EUR][1000 genomes]
rs4764369	0.87[CEU][hapmap];0.81[ASN][1000 genomes]
rs71450031	0.84[EUR][1000 genomes]
rs71450032	0.84[EUR][1000 genomes]
rs765792	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs7958472	0.85[CEU][hapmap];0.81[ASN][1000 genomes]
rs7969664	0.81[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	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1054811	chr12:10350587-10440005	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10366800-10386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:10368400-10380200	Weak transcription	GM12878-XiMat	blood
3	chr12:10368400-10380400	Weak transcription	Dnd41	blood
4	chr12:10372800-10379600	Weak transcription	Right Atrium	heart
5	chr12:10373400-10382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:10375200-10379600	Weak transcription	Thymus	Thymus
7	chr12:10375200-10380000	Weak transcription	Small Intestine	intestine
8	chr12:10375400-10379600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:10375400-10380600	Weak transcription	Fetal Lung	lung
10	chr12:10375600-10380400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:10376000-10379600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:10376400-10380200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:10376400-10380200	Weak transcription	Gastric	stomach
14	chr12:10376400-10380400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:10376400-10380400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:10376400-10386600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:10376400-10386600	Weak transcription	Brain Substantia Nigra	brain
18	chr12:10376400-10388600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:10376400-10395000	Weak transcription	Pancreas	Pancrea
20	chr12:10376400-10397600	Weak transcription	Aorta	Aorta
21	chr12:10376600-10379200	Weak transcription	HUVEC	blood vessel
22	chr12:10376600-10380000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:10376600-10380400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:10376600-10382400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:10376600-10385600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:10376800-10379200	Weak transcription	Fetal Brain Male	brain
27	chr12:10376800-10380000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:10376800-10380400	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:10376800-10385800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:10377000-10379400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:10377000-10380000	Weak transcription	Primary T cells from cord blood	blood
32	chr12:10377000-10380200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:10377000-10382800	Weak transcription	Right Ventricle	heart
34	chr12:10377000-10385000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:10377000-10386600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:10377200-10379600	Weak transcription	Adipose Nuclei	Adipose
37	chr12:10377200-10380200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:10377200-10380200	Weak transcription	Brain Anterior Caudate	brain
39	chr12:10377200-10381800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr12:10377200-10383000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:10377200-10384200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:10377200-10385200	Weak transcription	Lung	lung
43	chr12:10377200-10386000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:10377200-10386000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:10377200-10386000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr12:10377200-10386800	Weak transcription	HSMMtube	muscle
47	chr12:10377200-10389000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:10377200-10394200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:10377200-10394600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr12:10377200-10399000	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links