Variant report

Variant	rs11551400
Chromosome Location	chr2:96914636-96914637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96872434..96874622-chr2:96912673..96915049,2	MCF-7	breast:
2	chr2:96914494..96917084-chr2:96925071..96927865,2	MCF-7	breast:
3	chr2:96794272..96796392-chr2:96913963..96916568,2	MCF-7	breast:
4	chr2:96906615..96908576-chr2:96914458..96917138,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000135956	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1048675	0.88[YRI][hapmap]
rs11886999	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11903461	0.91[ASW][hapmap];0.88[YRI][hapmap]
rs12613263	0.83[EUR][1000 genomes]
rs12617019	0.89[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs12618133	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs17479466	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs2016759	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276650	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2305935	0.91[ASW][hapmap];0.88[YRI][hapmap]
rs3214058	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs3214063	0.83[ASW][hapmap];0.88[YRI][hapmap]
rs3852673	0.84[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4371393	0.89[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs4592891	0.86[EUR][1000 genomes]
rs4826	0.89[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs4907307	0.88[YRI][hapmap]
rs4907310	0.91[ASW][hapmap];0.83[YRI][hapmap]
rs4907311	0.91[ASW][hapmap];0.88[YRI][hapmap]
rs57251156	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57476471	0.86[EUR][1000 genomes]
rs59664047	0.86[EUR][1000 genomes]
rs61697794	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62153010	0.84[EUR][1000 genomes]
rs62153014	0.86[EUR][1000 genomes]
rs62153018	0.86[EUR][1000 genomes]
rs62153020	0.85[EUR][1000 genomes]
rs62153022	0.85[EUR][1000 genomes]
rs62153029	0.85[EUR][1000 genomes]
rs6576968	0.83[GIH][hapmap];0.86[TSI][hapmap]
rs6725867	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6725872	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6737429	0.91[ASW][hapmap];0.88[YRI][hapmap]
rs72825854	0.84[EUR][1000 genomes]
rs72825856	0.84[EUR][1000 genomes]
rs72825864	0.85[EUR][1000 genomes]
rs72825877	0.85[EUR][1000 genomes]
rs7579553	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7579709	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs7580178	0.86[EUR][1000 genomes]
rs997547	0.86[TSI][hapmap]
rs997548	0.89[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][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	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11551400	AC008268.2	cis	Nerve Tibial	GTEx
rs11551400	FER1L5	cis	parietal	SCAN
rs11551400	AC008268.2	cis	Artery Tibial	GTEx
rs11551400	ANKRD36B	cis	cerebellum	SCAN
rs11551400	TEKT4	cis	cerebellum	SCAN
rs11551400	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs11551400	CIAO1	cis	lymphoblastoid	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96876000-96915200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:96876200-96916000	Weak transcription	Dnd41	blood
3	chr2:96876200-96917800	Weak transcription	Brain Angular Gyrus	brain
4	chr2:96877800-96916000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:96889600-96915800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:96891200-96916200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:96891400-96916400	Weak transcription	HSMM	muscle
8	chr2:96896200-96917600	Weak transcription	Pancreas	Pancrea
9	chr2:96899600-96918800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:96900000-96917800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:96900400-96917600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:96902600-96917600	Weak transcription	Fetal Lung	lung
13	chr2:96904200-96917600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:96905000-96917400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:96905200-96918200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:96905400-96917200	Weak transcription	Fetal Brain Female	brain
17	chr2:96905600-96917400	Weak transcription	Brain Germinal Matrix	brain
18	chr2:96905800-96915200	Weak transcription	HSMMtube	muscle
19	chr2:96905800-96916000	Weak transcription	Gastric	stomach
20	chr2:96905800-96917200	Weak transcription	HepG2	liver
21	chr2:96905800-96917800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:96905800-96918400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:96906800-96915200	Weak transcription	Fetal Intestine Large	intestine
24	chr2:96906800-96917600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:96907000-96916000	Weak transcription	Aorta	Aorta
26	chr2:96907000-96917600	Weak transcription	Fetal Brain Male	brain
27	chr2:96907200-96915200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:96907400-96915200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:96907400-96917800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:96907400-96918800	Weak transcription	Small Intestine	intestine
31	chr2:96908000-96915800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:96908000-96917600	Weak transcription	Esophagus	oesophagus
33	chr2:96908000-96917600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:96908200-96915600	Weak transcription	Right Atrium	heart
35	chr2:96908200-96917600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:96908200-96917600	Weak transcription	Colonic Mucosa	Colon
37	chr2:96908400-96915200	Weak transcription	Thymus	Thymus
38	chr2:96908400-96915400	Weak transcription	Brain Substantia Nigra	brain
39	chr2:96908400-96916600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:96908400-96917600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:96908600-96915200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:96908600-96917200	Weak transcription	NHEK	skin
43	chr2:96908600-96917600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:96908600-96917600	Weak transcription	Brain Anterior Caudate	brain
45	chr2:96908600-96917600	Weak transcription	Brain Hippocampus Middle	brain
46	chr2:96908600-96917600	Weak transcription	HMEC	breast
47	chr2:96908600-96917800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:96908800-96916200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:96909000-96916000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:96909000-96916000	Weak transcription	Fetal Thymus	thymus

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