Variant report

Variant	rs12646621
Chromosome Location	chr4:6934053-6934054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10009332	0.88[ASN][1000 genomes]
rs10012305	0.89[ASN][1000 genomes]
rs10019900	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10937762	0.82[ASN][1000 genomes]
rs10937766	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10937769	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10937771	0.88[ASN][1000 genomes]
rs11723686	0.87[ASN][1000 genomes]
rs11731681	0.86[ASN][1000 genomes]
rs11732389	0.88[ASN][1000 genomes]
rs11942739	0.83[ASN][1000 genomes]
rs12512922	0.84[ASN][1000 genomes]
rs12646620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114976	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13435015	0.83[ASN][1000 genomes]
rs28392702	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28463777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28523495	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601619	0.81[ASN][1000 genomes]
rs28703753	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34760356	0.85[ASN][1000 genomes]
rs35296019	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35490604	0.87[ASN][1000 genomes]
rs3892976	0.84[ASN][1000 genomes]
rs4234790	0.87[ASN][1000 genomes]
rs4290891	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4315786	0.84[ASN][1000 genomes]
rs4484301	0.87[ASN][1000 genomes]
rs4513567	0.88[ASN][1000 genomes]
rs4608812	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4689055	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4689558	0.85[ASN][1000 genomes]
rs4689562	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446550	0.80[ASN][1000 genomes]
rs6446551	0.80[ASN][1000 genomes]
rs6446552	0.80[ASN][1000 genomes]
rs6834007	0.86[ASN][1000 genomes]
rs6852468	0.94[ASN][1000 genomes]
rs7657702	0.84[ASN][1000 genomes]
rs7668186	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7689337	0.80[ASN][1000 genomes]
rs9291121	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9291122	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9291123	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9291124	0.80[AFR][1000 genomes]
rs9999127	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv980396	chr4:6929613-6942211	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6919600-6942200	Weak transcription	Hela-S3	cervix
2	chr4:6920200-6939600	Weak transcription	HUVEC	blood vessel
3	chr4:6926200-6942000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:6926200-6942600	Weak transcription	NHEK	skin
5	chr4:6926200-6943200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:6926600-6935000	Enhancers	Liver	Liver
7	chr4:6926600-6939200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:6928000-6934600	Weak transcription	Esophagus	oesophagus
9	chr4:6928000-6937400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:6928000-6939200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:6928000-6942000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:6928000-6969600	Weak transcription	Aorta	Aorta
13	chr4:6929000-6934200	Weak transcription	Fetal Stomach	stomach
14	chr4:6929000-6936800	Weak transcription	A549	lung
15	chr4:6929000-6942000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:6929000-6942200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:6929200-6942000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr4:6929400-6942400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:6929600-6934200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:6929600-6934400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:6929600-6942400	Weak transcription	Small Intestine	intestine
22	chr4:6929800-6934400	Weak transcription	GM12878-XiMat	blood
23	chr4:6929800-6939200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:6929800-6943200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:6930000-6940400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:6930600-6939200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:6931200-6935400	Weak transcription	Gastric	stomach
28	chr4:6931400-6937800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:6931400-6940000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:6931400-6943200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:6931600-6937800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:6931600-6940800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr4:6931600-6942000	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:6931800-6935800	Strong transcription	K562	blood
35	chr4:6932000-6934200	Weak transcription	Brain Angular Gyrus	brain
36	chr4:6932000-6934200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:6932000-6934400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:6932000-6935600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:6932000-6939200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:6932000-6939200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:6932000-6939800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:6932000-6940000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:6932000-6941600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:6932000-6942000	Weak transcription	Stomach Mucosa	stomach
45	chr4:6932000-6943400	Weak transcription	Fetal Brain Female	brain
46	chr4:6932000-6943400	Weak transcription	Fetal Kidney	kidney
47	chr4:6932200-6934200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr4:6932200-6934200	Weak transcription	Brain Anterior Caudate	brain
49	chr4:6932200-6934200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr4:6932200-6934200	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links