Variant report

Variant	rs2267755
Chromosome Location	chr14:78139025-78139026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78137716..78140274-chr14:78142246..78143787,2	MCF-7	breast:
2	chr14:78138709..78140424-chr14:78170369..78172653,2	MCF-7	breast:
3	chr14:78133661..78136302-chr14:78138970..78141654,2	K562	blood:
4	chr14:78136536..78139253-chr14:78155471..78158284,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100601	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1008989	0.91[CHB][hapmap]
rs1011111	0.83[AMR][1000 genomes]
rs10483885	0.81[CEU][hapmap]
rs1076496	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11159294	0.83[MEX][hapmap]
rs12432030	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12587155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12587584	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12587825	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12880300	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs12880840	0.81[ASN][1000 genomes]
rs12881898	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12886631	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12889788	0.86[CHB][hapmap]
rs12891621	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12892669	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1477264	0.81[CEU][hapmap]
rs2080816	0.83[MEX][hapmap]
rs2267757	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2270443	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2299931	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35261431	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35657726	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4540996	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4899673	0.81[CEU][hapmap]
rs4899676	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4903624	0.96[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4903644	0.81[ASN][1000 genomes]
rs67408612	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7145979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs726538	0.83[MEX][hapmap]
rs72688831	0.81[ASN][1000 genomes]
rs8003389	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8003715	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking 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	20 gene(s)	inside rSNPs	diseases
2	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv869872	chr14:78119527-78161340	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	esv3693172	chr14:78130479-78152921	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv9156	chr14:78138141-78140714	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2267755	RPS6KL1	cis	cerebellum	SCAN
rs2267755	ADCK1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78121400-78139800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr14:78121800-78139800	Weak transcription	Gastric	stomach
3	chr14:78122000-78139600	Weak transcription	Fetal Intestine Large	intestine
4	chr14:78122000-78139800	Weak transcription	Pancreas	Pancrea
5	chr14:78125400-78139800	Weak transcription	Right Ventricle	heart
6	chr14:78126800-78139800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr14:78126800-78139800	Weak transcription	Spleen	Spleen
8	chr14:78127400-78139800	Weak transcription	Lung	lung
9	chr14:78127400-78173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr14:78127600-78139200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr14:78127600-78139200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:78127600-78139800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr14:78127600-78140000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:78127600-78140000	Weak transcription	Esophagus	oesophagus
15	chr14:78127800-78139600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr14:78127800-78139800	Weak transcription	Brain Germinal Matrix	brain
17	chr14:78128000-78157800	Weak transcription	Fetal Brain Male	brain
18	chr14:78128200-78139600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr14:78129000-78139800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:78129200-78139600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr14:78129800-78147600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr14:78130000-78139800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr14:78130200-78139400	Weak transcription	HUVEC	blood vessel
24	chr14:78130200-78139600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:78130400-78139200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr14:78130400-78139400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr14:78130400-78139400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr14:78130400-78139600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr14:78130400-78139800	Weak transcription	Hela-S3	cervix
30	chr14:78130400-78139800	Weak transcription	NHEK	skin
31	chr14:78130400-78140200	Weak transcription	HMEC	breast
32	chr14:78130600-78139200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr14:78130600-78139600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr14:78130800-78139200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr14:78131600-78139200	Weak transcription	Aorta	Aorta
36	chr14:78132000-78139200	Weak transcription	Fetal Kidney	kidney
37	chr14:78133400-78139800	Weak transcription	Osteobl	bone
38	chr14:78133800-78139800	Weak transcription	HSMM	muscle
39	chr14:78133800-78140400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr14:78134200-78148000	Weak transcription	NH-A	brain
41	chr14:78134400-78139800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr14:78134400-78163400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr14:78134600-78139600	Weak transcription	Brain Angular Gyrus	brain
44	chr14:78135000-78139600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr14:78135000-78140000	Weak transcription	Fetal Intestine Small	intestine
46	chr14:78135200-78139800	Weak transcription	Fetal Stomach	stomach
47	chr14:78135200-78156200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr14:78135400-78139600	Weak transcription	Thymus	Thymus
49	chr14:78136200-78139800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr14:78136200-78139800	Weak transcription	Rectal Mucosa Donor 31	rectum

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