Variant report

Variant	rs12402397
Chromosome Location	chr1:212395944-212395945
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212394433..212396224-chr1:212398740..212401214,2	K562	blood:
2	chr1:212393346..212396328-chr1:212457940..212460726,2	K562	blood:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction
ENSG00000226251	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1009622	0.83[CHB][hapmap]
rs10863953	0.86[EUR][1000 genomes]
rs10863954	0.87[EUR][1000 genomes]
rs11119879	0.87[EUR][1000 genomes]
rs11119880	0.82[EUR][1000 genomes]
rs11119883	0.89[EUR][1000 genomes]
rs11119884	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119887	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12028026	0.89[EUR][1000 genomes]
rs12038888	0.81[EUR][1000 genomes]
rs12073206	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12746096	0.80[EUR][1000 genomes]
rs1389369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389370	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1389371	0.83[CHB][hapmap]
rs1472226	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967114	0.87[EUR][1000 genomes]
rs1967116	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1967117	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001234	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2087946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307128	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2884512	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351386	0.83[CHB][hapmap]
rs351408	0.83[JPT][hapmap]
rs35209719	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816912	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4362041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4500383	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4558048	0.87[EUR][1000 genomes]
rs4951581	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951582	0.84[ASN][1000 genomes]
rs6540729	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6540731	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540734	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540735	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6668866	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6679796	0.82[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695681	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7511781	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7515645	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518329	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7519168	0.81[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530375	0.87[EUR][1000 genomes]
rs7537062	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7542973	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544225	0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7552021	0.89[EUR][1000 genomes]
rs867584	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903120	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs903121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs951623	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12402397	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs12402397	TMEM206	cis	Esophagus Mucosa	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212391200-212399000	Weak transcription	Pancreas	Pancrea
2	chr1:212392000-212396000	Enhancers	K562	blood
3	chr1:212392000-212399400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:212392200-212398600	Weak transcription	Right Ventricle	heart
5	chr1:212392200-212399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:212392200-212399200	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:212392400-212397800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:212392400-212398600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:212392600-212397400	Weak transcription	Adipose Nuclei	Adipose
10	chr1:212392600-212399000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:212392600-212399200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:212392600-212404800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:212393200-212398600	Weak transcription	Primary T cells from cord blood	blood
14	chr1:212393400-212398800	Weak transcription	Stomach Mucosa	stomach
15	chr1:212393600-212398600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:212393600-212398600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:212393600-212398800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:212393600-212398800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:212393600-212399200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:212393600-212399200	Weak transcription	Small Intestine	intestine
21	chr1:212393800-212398200	Weak transcription	Fetal Thymus	thymus
22	chr1:212393800-212398600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:212393800-212399000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:212393800-212399000	Weak transcription	Fetal Heart	heart
25	chr1:212394800-212399200	Weak transcription	Gastric	stomach
26	chr1:212395000-212397400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:212395200-212399000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:212395200-212399000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:212395200-212399200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:212395400-212398600	Weak transcription	Fetal Kidney	kidney
31	chr1:212395400-212398800	Weak transcription	Fetal Lung	lung
32	chr1:212395400-212399000	Weak transcription	Spleen	Spleen
33	chr1:212395400-212399200	Weak transcription	Left Ventricle	heart
34	chr1:212395600-212397600	Weak transcription	Lung	lung
35	chr1:212395600-212399200	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links