Variant report

Variant	rs3794224
Chromosome Location	chr12:105623770-105623771
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105501229..105503953-chr12:105621352..105624637,3	MCF-7	breast:
2	chr12:105608225..105613366-chr12:105619333..105624104,5	MCF-7	breast:
3	chr12:105620755..105625323-chr12:105625745..105629848,5	K562	blood:

Variant related genes	Relation type
ENSG00000235162	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1014502	0.85[EUR][1000 genomes]
rs10431460	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1057110	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1077896	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10861359	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10861361	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10861363	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1109433	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11112369	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11112370	0.84[EUR][1000 genomes]
rs11112372	0.81[EUR][1000 genomes]
rs11112375	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11112376	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11112379	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11112388	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11112409	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11112412	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11112415	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11112416	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112421	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112423	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112432	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11112433	0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11831854	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11832489	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11834277	0.84[EUR][1000 genomes]
rs12228093	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12228948	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12812433	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12815031	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12819309	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12830078	0.80[AFR][1000 genomes]
rs1317955	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1373552	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1444611	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1470381	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2272495	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2293643	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2293644	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28549976	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34075890	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34983773	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35462155	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35672903	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3736628	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3794222	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3794223	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3794227	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3817607	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3829296	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964125	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964128	0.81[ASN][1000 genomes]
rs4964334	0.81[EUR][1000 genomes]
rs4964335	0.85[EUR][1000 genomes]
rs4964336	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4964338	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4964339	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4964340	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4964342	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4964347	0.81[ASN][1000 genomes]
rs56693261	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73179994	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7484699	0.82[ASN][1000 genomes]
rs7485364	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7487098	0.82[ASN][1000 genomes]
rs755604	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8015	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs881279	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9919746	0.84[EUR][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	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:105600800-105626800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:105605600-105628400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:105609200-105626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:105609200-105628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:105611200-105628200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:105611600-105626200	Weak transcription	Fetal Brain Male	brain
9	chr12:105612000-105624800	Genic enhancers	NHDF-Ad	bronchial
10	chr12:105612800-105624200	Strong transcription	Fetal Stomach	stomach
11	chr12:105616600-105629000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:105617000-105629000	Weak transcription	Esophagus	oesophagus
13	chr12:105617400-105625400	Genic enhancers	Muscle Satellite Cultured Cells	--
14	chr12:105617400-105629000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:105617600-105625400	Strong transcription	A549	lung
16	chr12:105618200-105625200	Weak transcription	Right Ventricle	heart
17	chr12:105618600-105625200	Weak transcription	Spleen	Spleen
18	chr12:105618600-105626800	Weak transcription	Gastric	stomach
19	chr12:105619400-105625200	Genic enhancers	HSMM	muscle
20	chr12:105619400-105627400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:105620000-105625800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:105620400-105624400	Weak transcription	Right Atrium	heart
23	chr12:105620400-105624600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:105620400-105624800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:105620400-105625000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:105620400-105625200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:105620400-105625200	Weak transcription	Pancreas	Pancrea
28	chr12:105620400-105625400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr12:105620400-105625400	Weak transcription	Fetal Heart	heart
30	chr12:105620400-105626000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:105620400-105626600	Weak transcription	Psoas Muscle	Psoas
32	chr12:105620600-105624200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr12:105620600-105624600	Genic enhancers	NH-A	brain
34	chr12:105620600-105625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr12:105621200-105624600	Enhancers	HUVEC	blood vessel
36	chr12:105621200-105625200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr12:105621200-105625800	Strong transcription	Primary B cells from cord blood	blood
38	chr12:105621200-105626200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr12:105621600-105624600	Enhancers	Brain Substantia Nigra	brain
40	chr12:105621600-105625200	Weak transcription	Ovary	ovary
41	chr12:105621600-105627200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:105621800-105625200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:105621800-105625400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:105621800-105626400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:105621800-105626800	Enhancers	Brain Anterior Caudate	brain
46	chr12:105621800-105626800	Weak transcription	Fetal Kidney	kidney
47	chr12:105621800-105628600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:105621800-105628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:105622000-105625200	Weak transcription	Lung	lung
50	chr12:105622000-105627400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links