Variant report

Variant	rs6414764
Chromosome Location	chr4:15626475-15626476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15607476..15609952-chr4:15624488..15626808,2	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10005305	0.94[AFR][1000 genomes]
rs10008878	0.96[AFR][1000 genomes]
rs10009089	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015827	0.81[ASN][1000 genomes]
rs10017222	1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs10025875	0.96[AFR][1000 genomes]
rs10034315	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433813	0.81[ASN][1000 genomes]
rs10516289	1.00[CHB][hapmap]
rs11722757	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723554	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs11726647	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11729955	1.00[CHB][hapmap]
rs11732953	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11735063	0.86[CHB][hapmap]
rs12642407	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12650529	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106528	0.88[JPT][hapmap]
rs13131119	0.86[JPT][hapmap]
rs13134177	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13141724	0.85[JPT][hapmap]
rs13144428	0.86[JPT][hapmap]
rs13150957	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1468735	0.86[JPT][hapmap]
rs1468736	0.82[JPT][hapmap]
rs16892135	0.86[JPT][hapmap]
rs16892143	0.86[JPT][hapmap]
rs16892156	0.82[JPT][hapmap]
rs17405811	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs17476642	1.00[CHB][hapmap]
rs17476670	0.86[JPT][hapmap]
rs1786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2041672	0.86[JPT][hapmap]
rs2041673	0.86[JPT][hapmap]
rs28394730	0.97[AFR][1000 genomes]
rs28402170	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28447067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28644177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28820655	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34473224	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34559117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34831330	0.86[JPT][hapmap]
rs34955342	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35013326	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35120298	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3775956	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3775957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41417147	0.86[JPT][hapmap]
rs4257653	0.96[ASN][1000 genomes]
rs4267734	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs4301111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4326008	0.86[JPT][hapmap]
rs4331772	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4396986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4423870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4549375	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4554069	0.97[AFR][1000 genomes]
rs4600905	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698116	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6449150	0.86[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs6449152	0.81[ASN][1000 genomes]
rs6815254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6815296	1.00[CHB][hapmap]
rs6816982	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6823775	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825051	0.88[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs6825815	0.86[JPT][hapmap]
rs6826058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827406	1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs6828776	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835038	0.88[JPT][hapmap]
rs6839654	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6843740	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6844141	0.88[JPT][hapmap]
rs6848779	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6852735	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857442	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7434484	1.00[CHB][hapmap]
rs7667175	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7698596	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9994518	0.85[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv518830	chr4:15610771-15672200	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3376437	chr4:15613963-15626944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3464784	chr4:15613969-15626901	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3464785	chr4:15613969-15626901	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6414764	LOC285550	cis	lesional skin	skin_eQTL
rs6414764	LOC285550	cis	normal skin	skin_eQTL
rs6414764	LOC285550	cis	uninvolved skin	skin_eQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15568400-15655600	Weak transcription	Gastric	stomach
2	chr4:15600800-15653000	Weak transcription	Colonic Mucosa	Colon
3	chr4:15601000-15651600	Weak transcription	Small Intestine	intestine
4	chr4:15602600-15655600	Weak transcription	Pancreas	Pancrea
5	chr4:15603800-15626800	Weak transcription	NHLF	lung
6	chr4:15605800-15650200	Weak transcription	Stomach Mucosa	stomach
7	chr4:15606000-15633800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:15613400-15635000	Weak transcription	HSMMtube	muscle
9	chr4:15617800-15627400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:15618600-15627000	Weak transcription	Right Ventricle	heart
11	chr4:15618600-15651000	Weak transcription	Spleen	Spleen
12	chr4:15620800-15626800	Weak transcription	Lung	lung
13	chr4:15621000-15632600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:15621600-15627000	Weak transcription	Brain Angular Gyrus	brain
15	chr4:15621800-15626800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:15621800-15626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:15621800-15626800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:15621800-15627000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:15621800-15627000	Weak transcription	Esophagus	oesophagus
20	chr4:15621800-15627000	Weak transcription	Psoas Muscle	Psoas
21	chr4:15622200-15655400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:15622400-15638000	Weak transcription	HepG2	liver
23	chr4:15622400-15639600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:15622600-15626800	Weak transcription	Fetal Brain Female	brain
25	chr4:15622600-15627000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:15622600-15629200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr4:15622600-15645800	Weak transcription	Aorta	Aorta
28	chr4:15622800-15635200	Weak transcription	Fetal Stomach	stomach
29	chr4:15623200-15626600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:15623200-15627000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:15623400-15626800	Weak transcription	Fetal Heart	heart
32	chr4:15623400-15638000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr4:15623600-15627000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:15623800-15626600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:15623800-15626600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:15623800-15626600	Weak transcription	Left Ventricle	heart
37	chr4:15623800-15626600	Weak transcription	Right Atrium	heart
38	chr4:15623800-15627000	Weak transcription	Ovary	ovary
39	chr4:15623800-15627000	Weak transcription	Thymus	Thymus
40	chr4:15623800-15627800	Strong transcription	Primary hematopoietic stem cells	blood
41	chr4:15623800-15633800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:15623800-15635200	Weak transcription	Fetal Intestine Small	intestine
43	chr4:15623800-15635400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:15624200-15636000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:15624400-15626600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr4:15624400-15626800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr4:15624400-15627600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr4:15624400-15629600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:15624400-15629800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:15624600-15626600	Weak transcription	K562	blood

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