Variant report

Variant	rs7575613
Chromosome Location	chr2:183779535-183779536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:183764300..183766706-chr2:183778634..183780515,2	MCF-7	breast:
2	chr2:183767158..183769431-chr2:183778659..183782092,3	K562	blood:
3	chr2:183778975..183782738-chr2:183784220..183787705,4	K562	blood:
4	chr2:183771103..183773642-chr2:183778453..183781754,3	K562	blood:
5	chr2:183773913..183775803-chr2:183777634..183779722,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17265880	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2675089	0.83[EUR][1000 genomes]
rs35142583	0.91[AFR][1000 genomes]
rs66727515	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6711655	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6734848	0.90[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6739840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72886535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72886536	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72886547	0.91[AFR][1000 genomes]
rs72886597	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72888442	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72888444	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72888445	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72888452	0.84[AFR][1000 genomes]
rs72888453	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72888459	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72888467	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72888485	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72888487	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7595898	1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7602601	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757842	chr2:183437700-183835084	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759104	chr2:183437700-183835084	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv34847	chr2:183537399-183786763	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv818096	chr2:183701588-183827018	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer 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 target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7575613	NCKAP1	Cis_1M	lymphoblastoid	RTeQTL
rs7575613	NCKAP1	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183757400-183797800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:183765200-183792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:183765600-183805200	Weak transcription	Gastric	stomach
4	chr2:183768600-183779800	Weak transcription	Fetal Heart	heart
5	chr2:183768600-183811600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:183769800-183811800	Weak transcription	Small Intestine	intestine
7	chr2:183770600-183786000	Weak transcription	Brain Substantia Nigra	brain
8	chr2:183770800-183779600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:183770800-183787200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:183772400-183779600	Strong transcription	HSMM	muscle
11	chr2:183772400-183780000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:183772400-183791000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:183772400-183799200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:183772400-183811800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:183772800-183779600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:183772800-183780000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:183772800-183786200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:183773200-183779600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:183773400-183779800	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:183773400-183781000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:183773400-183866000	Weak transcription	Colonic Mucosa	Colon
22	chr2:183773400-183877800	Weak transcription	Stomach Mucosa	stomach
23	chr2:183773600-183779600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:183773600-183785000	Weak transcription	Fetal Kidney	kidney
25	chr2:183773600-183793000	Weak transcription	Fetal Brain Male	brain
26	chr2:183773800-183779600	Weak transcription	Brain Angular Gyrus	brain
27	chr2:183773800-183779800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:183773800-183779800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:183774000-183779800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:183774400-183779800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:183774800-183779600	Strong transcription	NH-A	brain
32	chr2:183775000-183787000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:183775200-183784400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:183775400-183779600	Weak transcription	Esophagus	oesophagus
35	chr2:183775600-183833000	Weak transcription	Pancreas	Pancrea
36	chr2:183775800-183779600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:183775800-183779800	Strong transcription	NHDF-Ad	bronchial
38	chr2:183776000-183779600	Weak transcription	Right Ventricle	heart
39	chr2:183776000-183783600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:183776000-183785000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:183776200-183786000	Weak transcription	Aorta	Aorta
42	chr2:183777000-183779600	Strong transcription	HSMMtube	muscle
43	chr2:183777000-183780400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:183777000-183782200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:183777000-183783200	Strong transcription	Fetal Intestine Large	intestine
46	chr2:183777200-183780600	Strong transcription	Ovary	ovary
47	chr2:183777200-183780600	Weak transcription	A549	lung
48	chr2:183777200-183780800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr2:183777400-183779600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr2:183777600-183779600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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