Variant report

Variant	rs11676737
Chromosome Location	chr2:46929873-46929874
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46929305..46931756-chr2:46933052..46934727,2	MCF-7	breast:
2	chr2:46924915..46928636-chr2:46928946..46932522,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1058157	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1109380	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11695058	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12474201	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12998753	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12998762	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13025595	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13025984	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031872	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13429704	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17822019	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17822294	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2346878	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34401107	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35158352	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35722922	0.89[AMR][1000 genomes]
rs35825831	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829835	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4952842	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4952843	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4953419	0.83[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6738426	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7562173	0.84[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7584870	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7594523	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs897530	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
4	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46925000-46930000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr2:46925800-46930200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:46925800-46930200	Active TSS	NHLF	lung
4	chr2:46927200-46935800	Weak transcription	Spleen	Spleen
5	chr2:46927400-46931400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:46927400-46932000	Weak transcription	Gastric	stomach
7	chr2:46927400-46932000	Weak transcription	Pancreas	Pancrea
8	chr2:46927400-46933400	Weak transcription	Brain Angular Gyrus	brain
9	chr2:46927400-46933800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:46927600-46930000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:46927600-46930600	Enhancers	Small Intestine	intestine
12	chr2:46927600-46930800	Weak transcription	Colonic Mucosa	Colon
13	chr2:46927600-46931400	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:46927600-46931600	Weak transcription	Stomach Mucosa	stomach
15	chr2:46927600-46932800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:46927800-46930600	Enhancers	Fetal Lung	lung
17	chr2:46927800-46931000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:46927800-46931000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:46927800-46940000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:46928000-46931000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:46928000-46931000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:46928000-46931200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:46928000-46931800	Weak transcription	Aorta	Aorta
24	chr2:46928000-46931800	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:46928000-46943600	Weak transcription	Thymus	Thymus
26	chr2:46928200-46930000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:46928400-46930000	Flanking Active TSS	A549	lung
28	chr2:46928400-46931000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr2:46928400-46932200	Weak transcription	HSMM	muscle
30	chr2:46928600-46930600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr2:46928600-46930600	Weak transcription	Primary B cells from cord blood	blood
32	chr2:46928600-46931000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:46928600-46931600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:46928600-46932400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:46928600-46933600	Weak transcription	Brain Substantia Nigra	brain
36	chr2:46928600-46933600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:46928600-46934000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:46928600-46944400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:46928800-46930000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:46928800-46930200	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr2:46928800-46930400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr2:46928800-46930400	Weak transcription	Primary T cells from cord blood	blood
43	chr2:46928800-46930600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr2:46928800-46931000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr2:46928800-46931000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:46928800-46931600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:46928800-46932000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:46928800-46932000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:46928800-46932000	Weak transcription	Left Ventricle	heart
50	chr2:46928800-46932200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links