Variant report

Variant	rs12623330
Chromosome Location	chr2:39065649-39065650
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39064983..39068575-chr2:39101517..39104346,3	MCF-7	breast:
2	chr2:39065545..39067577-chr2:39069948..39073607,4	K562	blood:

Variant related genes	Relation type
ENSG00000163214	Chromatin interaction
ENSG00000188010	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10173118	0.92[JPT][hapmap]
rs10173240	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10176932	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs10779923	0.86[JPT][hapmap]
rs10865143	0.81[CEU][hapmap]
rs11124651	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11675110	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12373604	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12465365	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712621	0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs12712625	0.84[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs12712626	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12712627	0.84[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13029388	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13029406	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs13383541	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs1530852	1.00[JPT][hapmap]
rs1530853	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs17494315	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1901289	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs1979142	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs3099940	0.83[CHB][hapmap]
rs3099984	0.81[ASN][1000 genomes]
rs3099985	0.81[ASN][1000 genomes]
rs3099987	0.82[ASN][1000 genomes]
rs3099994	0.91[EUR][1000 genomes]
rs3099995	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3112149	0.82[ASN][1000 genomes]
rs3112159	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs373300	0.86[JPT][hapmap]
rs3770681	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4133043	0.80[AMR][1000 genomes]
rs4265996	0.81[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes]
rs4630748	0.80[CEU][hapmap]
rs4641916	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4670266	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4670267	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs4670899	0.81[CEU][hapmap];0.91[YRI][hapmap]
rs60012208	0.82[ASN][1000 genomes]
rs6710418	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6715866	0.81[CEU][hapmap]
rs6732083	0.81[AMR][1000 genomes]
rs6734584	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6738403	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6741088	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7419616	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7565111	0.86[JPT][hapmap]
rs7586929	0.84[AMR][1000 genomes]
rs7589162	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7598922	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
3	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
5	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:39038800-39102200	Weak transcription	Gastric	stomach
8	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
10	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
12	chr2:39040000-39069000	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:39042800-39080600	Weak transcription	Small Intestine	intestine
14	chr2:39043600-39079800	Weak transcription	Right Ventricle	heart
15	chr2:39046000-39073200	Weak transcription	Pancreas	Pancrea
16	chr2:39046200-39070200	Weak transcription	NHLF	lung
17	chr2:39050400-39072800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:39050400-39079800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:39050400-39079800	Weak transcription	Spleen	Spleen
20	chr2:39050400-39088000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:39051000-39068600	Weak transcription	HMEC	breast
22	chr2:39052200-39068600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:39053200-39068600	Weak transcription	Brain Substantia Nigra	brain
24	chr2:39053200-39069600	Weak transcription	HUVEC	blood vessel
25	chr2:39053800-39068200	Weak transcription	HSMM	muscle
26	chr2:39053800-39068400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:39053800-39068600	Weak transcription	Aorta	Aorta
28	chr2:39053800-39068800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:39053800-39080200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:39053800-39080600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:39054200-39076400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:39055000-39080000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:39055200-39068800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr2:39055200-39085600	Weak transcription	Psoas Muscle	Psoas
35	chr2:39055600-39071600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:39055600-39073200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:39055600-39080000	Weak transcription	NH-A	brain
38	chr2:39055600-39080600	Weak transcription	Hela-S3	cervix
39	chr2:39055600-39080600	Weak transcription	K562	blood
40	chr2:39055800-39071200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:39056600-39066000	Strong transcription	Primary T cells from cord blood	blood
42	chr2:39056600-39066000	Strong transcription	A549	lung
43	chr2:39057000-39086200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:39057200-39066600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr2:39057200-39067000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:39057200-39071400	Strong transcription	Fetal Muscle Trunk	muscle
47	chr2:39058000-39068400	Weak transcription	Brain Angular Gyrus	brain
48	chr2:39058000-39087800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:39059000-39066400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:39060000-39080000	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links