Variant report

Variant	rs2638044
Chromosome Location	chr3:112245295-112245296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF3	chr3:112245287-112245645	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATG3-1	chr3:112244395-112246989	NONHSAT091182

Variant related genes	Relation type
OR7E100P	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10934177	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386896	1.00[ASN][1000 genomes]
rs1388442	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472106	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472107	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488260	1.00[ASN][1000 genomes]
rs1488262	1.00[ASN][1000 genomes]
rs1491629	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532198	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552707	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814053	1.00[ASN][1000 genomes]
rs1817694	1.00[ASN][1000 genomes]
rs1844864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877362	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877364	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906519	1.00[ASN][1000 genomes]
rs2029317	1.00[ASN][1000 genomes]
rs2399431	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464612	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638025	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638030	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638033	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638034	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638036	1.00[ASN][1000 genomes]
rs2638038	1.00[YRI][hapmap]
rs2638041	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638043	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2668216	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2705510	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705520	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705524	1.00[ASN][1000 genomes]
rs2705551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705554	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705563	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933140	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2969894	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109033	0.86[ASN][1000 genomes]
rs62264580	0.83[ASN][1000 genomes]
rs6793232	1.00[ASN][1000 genomes]
rs7612851	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7618978	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901829	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs971832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
7	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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	39 gene(s)	inside rSNPs	diseases
8	nsv965197	chr3:112238965-112250194	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112227400-112269800	Weak transcription	Small Intestine	intestine
2	chr3:112231600-112246800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:112234000-112247600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:112237000-112245400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:112237000-112247000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:112237200-112245600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:112237200-112247400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:112237200-112254200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:112237400-112245400	Weak transcription	Primary B cells from cord blood	blood
11	chr3:112238000-112245800	Weak transcription	Primary T cells from cord blood	blood
12	chr3:112238200-112245600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:112238200-112245800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:112238200-112247000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:112238200-112247400	Weak transcription	GM12878-XiMat	blood
16	chr3:112238600-112245800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:112238600-112249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:112238800-112245600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:112238800-112246000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:112239800-112245800	Weak transcription	Brain Germinal Matrix	brain
22	chr3:112239800-112247200	Weak transcription	Lung	lung
23	chr3:112239800-112247400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:112239800-112247800	Weak transcription	Aorta	Aorta
25	chr3:112239800-112247800	Weak transcription	Esophagus	oesophagus
26	chr3:112240000-112245800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:112240400-112245800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:112240600-112246600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:112241000-112246400	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:112241000-112251600	Weak transcription	HUVEC	blood vessel
31	chr3:112241200-112245400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:112241200-112245800	Weak transcription	Brain Angular Gyrus	brain
33	chr3:112241400-112245600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:112241600-112245400	Weak transcription	Fetal Brain Female	brain
35	chr3:112241600-112245600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:112241600-112245600	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:112241600-112245600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:112241600-112245600	Weak transcription	Placenta	Placenta
39	chr3:112241600-112245800	Weak transcription	Fetal Intestine Large	intestine
40	chr3:112241600-112259400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr3:112241800-112245800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:112241800-112245800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:112242000-112247400	Weak transcription	Spleen	Spleen
44	chr3:112242000-112247800	Weak transcription	Gastric	stomach
45	chr3:112242000-112248400	Weak transcription	NHDF-Ad	bronchial
46	chr3:112242200-112245800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:112242200-112247000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:112242200-112247400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:112242200-112247600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:112242200-112248000	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links