Variant report

Variant	rs4073960
Chromosome Location	chr6:56548359-56548360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1024196	1.00[CHD][hapmap]
rs10498811	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11961342	0.91[AFR][1000 genomes]
rs11968575	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap]
rs11970648	1.00[CHD][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap]
rs13190784	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs13191164	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13192037	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs13192478	0.85[AFR][1000 genomes]
rs13196211	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13205013	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13206849	0.95[EUR][1000 genomes]
rs13213878	0.82[AFR][1000 genomes]
rs13219546	0.82[AFR][1000 genomes]
rs16888118	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16888124	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16888126	0.92[EUR][1000 genomes]
rs16888128	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16888130	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16888133	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16888171	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs17684511	0.95[EUR][1000 genomes]
rs17684553	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17684571	0.93[EUR][1000 genomes]
rs17684878	0.81[MEX][hapmap]
rs17751682	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs17751695	1.00[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1903332	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs2967960	0.84[AFR][1000 genomes]
rs3002003	0.81[AFR][1000 genomes]
rs3002006	0.84[AFR][1000 genomes]
rs3002009	0.84[AFR][1000 genomes]
rs3002010	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs3002011	0.81[YRI][hapmap]
rs34138864	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34576803	0.96[EUR][1000 genomes]
rs34703847	0.84[AFR][1000 genomes]
rs34724718	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34824960	0.88[AFR][1000 genomes]
rs35206656	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35408048	0.95[EUR][1000 genomes]
rs35619924	0.95[EUR][1000 genomes]
rs35637749	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35668437	0.95[EUR][1000 genomes]
rs35687635	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35920751	0.91[AFR][1000 genomes]
rs4072271	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4074101	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4074102	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4074103	0.94[CEU][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4262190	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4275049	0.82[AFR][1000 genomes]
rs4640889	0.82[AFR][1000 genomes]
rs5024547	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs55742092	0.91[EUR][1000 genomes]
rs56101897	0.95[EUR][1000 genomes]
rs59247267	0.87[AFR][1000 genomes]
rs62412526	0.95[EUR][1000 genomes]
rs62412528	0.95[EUR][1000 genomes]
rs62412531	0.95[EUR][1000 genomes]
rs62412532	0.95[EUR][1000 genomes]
rs6901176	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6918949	0.81[MEX][hapmap]
rs6924375	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6926134	0.83[AFR][1000 genomes]
rs71564848	0.96[EUR][1000 genomes]
rs71564849	0.93[EUR][1000 genomes]
rs7749100	1.00[CHD][hapmap]
rs7758867	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs7759479	0.81[LWK][hapmap];0.84[MKK][hapmap]
rs7760542	1.00[CHD][hapmap]
rs7761729	0.81[MEX][hapmap]
rs7767128	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7775134	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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 miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv432888	chr6:56507489-56560764	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4073960	LRRC1	cis	cerebellum	SCAN
rs4073960	DST	cis	cerebellum	SCAN
rs4073960	BMP5	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56526400-56549200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:56527000-56554400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:56529600-56553800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:56535200-56555200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:56535600-56548600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:56535600-56549200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:56537000-56551800	Weak transcription	Esophagus	oesophagus
8	chr6:56537200-56548600	Weak transcription	Colonic Mucosa	Colon
9	chr6:56537200-56553400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:56537200-56555200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:56537400-56548400	Weak transcription	Adipose Nuclei	Adipose
12	chr6:56537600-56552600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:56537600-56553600	Weak transcription	Fetal Stomach	stomach
14	chr6:56537800-56549400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:56538000-56549200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:56540000-56548400	Weak transcription	Hela-S3	cervix
17	chr6:56542800-56548400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:56543000-56548800	Weak transcription	HUVEC	blood vessel
19	chr6:56543000-56559400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:56544200-56549200	Weak transcription	Right Atrium	heart
21	chr6:56545600-56553400	Enhancers	Brain Hippocampus Middle	brain
22	chr6:56546200-56548400	Weak transcription	Gastric	stomach
23	chr6:56546200-56552400	Enhancers	Brain Substantia Nigra	brain
24	chr6:56546200-56564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:56546800-56555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr6:56547000-56548600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:56547000-56549800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr6:56547200-56549200	Enhancers	HepG2	liver
29	chr6:56547200-56552200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:56547200-56552400	Enhancers	Brain Angular Gyrus	brain
31	chr6:56547200-56553400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:56547200-56554000	Enhancers	Brain Cingulate Gyrus	brain
33	chr6:56547200-56557400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:56547400-56548400	Enhancers	Fetal Heart	heart
35	chr6:56547400-56548400	Genic enhancers	HSMM	muscle
36	chr6:56547400-56548600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:56547400-56548600	Genic enhancers	NHDF-Ad	bronchial
38	chr6:56547400-56549200	Enhancers	Fetal Intestine Small	intestine
39	chr6:56547400-56549600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr6:56547400-56549600	Enhancers	Colon Smooth Muscle	Colon
41	chr6:56547400-56552400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr6:56547400-56552400	Enhancers	Ovary	ovary
43	chr6:56547400-56552800	Enhancers	Brain Anterior Caudate	brain
44	chr6:56547400-56561600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:56547600-56549200	Weak transcription	Left Ventricle	heart
46	chr6:56547600-56549600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:56547600-56550400	Enhancers	Fetal Lung	lung
48	chr6:56547800-56549200	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:56547800-56549400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:56547800-56549600	Enhancers	Pancreatic Islets	Pancreatic Islet

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