Variant report

Variant	rs12307828
Chromosome Location	chr12:50139060-50139061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50134227..50139526-chr12:50218668..50224471,9	K562	blood:
2	chr12:50137650..50140394-chr12:50217891..50219857,2	MCF-7	breast:
3	chr12:50126958..50129574-chr12:50137567..50139944,2	K562	blood:
4	chr12:50137626..50141652-chr12:50149897..50153012,3	K562	blood:
5	chr12:50133925..50140140-chr12:50217980..50223924,8	K562	blood:
6	chr12:50038061..50039763-chr12:50138977..50140506,2	K562	blood:

Variant related genes	Relation type
ENSG00000258057	Chromatin interaction
ENSG00000167566	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1012874	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1049986	0.87[CEU][hapmap]
rs10506287	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506288	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169097	0.87[CEU][hapmap]
rs11169106	0.87[CEU][hapmap]
rs11169125	0.87[CEU][hapmap]
rs11169126	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169127	0.87[CEU][hapmap]
rs11169143	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169145	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830696	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834380	0.87[CEU][hapmap]
rs11836837	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837639	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299505	0.87[CEU][hapmap]
rs12306422	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306430	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306481	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310510	0.87[CEU][hapmap]
rs12313353	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12313354	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314795	1.00[CEU][hapmap]
rs12315524	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317778	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1317131	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470906	0.87[CEU][hapmap]
rs1574326	0.87[CEU][hapmap]
rs17123764	1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123927	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123970	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993398	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336058	0.87[CEU][hapmap]
rs2336447	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563	0.87[CEU][hapmap]
rs4584654	0.87[CEU][hapmap]
rs4641552	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55637397	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56737983	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56743994	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56906356	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56945609	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57291131	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58756176	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59261129	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60094911	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60126713	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60415769	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60613973	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61281663	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137976	0.87[CEU][hapmap]
rs7298080	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74086911	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087113	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087134	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74087188	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs74089557	0.86[ASN][1000 genomes]
rs74089564	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089566	1.00[ASN][1000 genomes]
rs74089570	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089573	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7487779	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7487854	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688	0.87[CEU][hapmap]
rs7952734	0.87[CEU][hapmap]
rs7953412	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964320	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967073	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7968302	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970674	0.87[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971176	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971369	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973498	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979262	0.85[CEU][hapmap]
rs9805063	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50136400-50140800	Weak transcription	Gastric	stomach
2	chr12:50136600-50146400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:50136800-50144200	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr12:50136800-50146600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr12:50137000-50139200	Enhancers	Brain Cingulate Gyrus	brain
6	chr12:50137000-50139200	Enhancers	Colon Smooth Muscle	Colon
7	chr12:50137000-50142000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:50137000-50142200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:50137000-50143800	Weak transcription	Colonic Mucosa	Colon
10	chr12:50137000-50146200	Weak transcription	HSMMtube	muscle
11	chr12:50137000-50147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:50137200-50139200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:50137200-50139200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:50137200-50139200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:50137200-50140200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr12:50137200-50146200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:50137200-50152000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:50137400-50139200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr12:50137400-50140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:50137400-50140800	Enhancers	Adipose Nuclei	Adipose
21	chr12:50137400-50141200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr12:50137400-50142000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:50137400-50143200	Strong transcription	Fetal Thymus	thymus
24	chr12:50137400-50146400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:50137400-50146400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:50137400-50146600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:50137400-50150800	Weak transcription	Fetal Brain Male	brain
28	chr12:50137600-50146200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr12:50137800-50142000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:50137800-50142200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:50137800-50142200	Weak transcription	HSMM	muscle
32	chr12:50137800-50143800	Weak transcription	Fetal Stomach	stomach
33	chr12:50137800-50144200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:50137800-50146200	Weak transcription	Fetal Kidney	kidney
35	chr12:50138000-50139200	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr12:50138000-50139200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:50138000-50141000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:50138000-50141000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:50138000-50143800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:50138200-50139200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:50138200-50139200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:50138200-50139200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr12:50138200-50139200	Genic enhancers	Left Ventricle	heart
44	chr12:50138200-50139200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
45	chr12:50138200-50146400	Weak transcription	Fetal Brain Female	brain
46	chr12:50138400-50139200	Genic enhancers	Primary T cells from cord blood	blood
47	chr12:50138400-50139200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:50138400-50139200	Strong transcription	Fetal Muscle Leg	muscle
49	chr12:50138400-50139600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:50138400-50141200	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links