Variant report

Variant	rs12636825
Chromosome Location	chr3:67555552-67555553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11919650	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11919747	0.91[EUR][1000 genomes]
rs11923127	0.86[EUR][1000 genomes]
rs11927204	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12488930	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12489287	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17046528	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17046546	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4371532	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs4856869	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4856870	0.83[AMR][1000 genomes]
rs4856872	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4856873	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4856874	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs4856875	0.86[EUR][1000 genomes]
rs5028414	0.85[EUR][1000 genomes]
rs56020437	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56246741	0.88[EUR][1000 genomes]
rs56361934	0.86[EUR][1000 genomes]
rs58093651	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61386974	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6548615	0.86[EUR][1000 genomes]
rs6768958	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6784255	0.86[EUR][1000 genomes]
rs72923195	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72924913	0.86[EUR][1000 genomes]
rs7623441	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1012416	chr3:67546244-67615531	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67488400-67566400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:67500800-67567000	Weak transcription	Pancreas	Pancrea
3	chr3:67504000-67559800	Weak transcription	Esophagus	oesophagus
4	chr3:67508200-67577600	Weak transcription	Spleen	Spleen
5	chr3:67511600-67560000	Weak transcription	Lung	lung
6	chr3:67511800-67565000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:67513200-67564800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:67513400-67567800	Weak transcription	NHLF	lung
9	chr3:67513600-67559800	Weak transcription	NHDF-Ad	bronchial
10	chr3:67514600-67559800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:67519800-67557400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:67520800-67559800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:67521600-67580400	Weak transcription	Stomach Mucosa	stomach
14	chr3:67524200-67567000	Weak transcription	Placenta	Placenta
15	chr3:67526800-67583200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:67528200-67564400	Weak transcription	Fetal Lung	lung
17	chr3:67528200-67564800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:67529000-67559200	Weak transcription	GM12878-XiMat	blood
19	chr3:67530200-67560200	Weak transcription	NHEK	skin
20	chr3:67531400-67576200	Weak transcription	HMEC	breast
21	chr3:67533200-67577000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:67533400-67577600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:67534400-67576400	Weak transcription	Aorta	Aorta
24	chr3:67534600-67560000	Weak transcription	Right Ventricle	heart
25	chr3:67534600-67566200	Weak transcription	Gastric	stomach
26	chr3:67534800-67560200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:67534800-67566200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:67535000-67578800	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:67537400-67559800	Weak transcription	Ovary	ovary
30	chr3:67537400-67579600	Weak transcription	Small Intestine	intestine
31	chr3:67537600-67560200	Weak transcription	HSMMtube	muscle
32	chr3:67537600-67566800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:67540800-67564400	Weak transcription	Fetal Kidney	kidney
34	chr3:67541400-67582000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:67542200-67559000	Strong transcription	Primary T cells from cord blood	blood
36	chr3:67542400-67564800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:67542400-67566400	Weak transcription	NH-A	brain
38	chr3:67543200-67566000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:67544200-67580200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:67544400-67567200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:67544600-67560200	Weak transcription	Psoas Muscle	Psoas
42	chr3:67544800-67577600	Weak transcription	Thymus	Thymus
43	chr3:67545400-67564400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:67546000-67560000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:67546200-67557200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:67546200-67560000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:67546200-67560000	Weak transcription	Fetal Intestine Small	intestine
48	chr3:67546400-67558400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:67546400-67565000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:67546600-67558200	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links