Variant report

Variant	rs6815254
Chromosome Location	chr4:15692058-15692059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:15682774..15685413-chr4:15691736..15693825,4	K562	blood:
2	chr4:15681921..15686275-chr4:15691863..15696153,5	MCF-7	breast:
3	chr4:15656248..15659090-chr4:15690576..15694462,3	MCF-7	breast:
4	chr4:15690253..15693117-chr4:15724608..15727161,2	MCF-7	breast:
5	chr4:15690443..15693747-chr4:15694264..15697002,4	MCF-7	breast:
6	chr4:15691991..15693828-chr4:15939773..15942027,2	MCF-7	breast:
7	chr4:15682706..15688918-chr4:15689234..15693729,6	K562	blood:
8	chr4:15685927..15688320-chr4:15691706..15694352,2	K562	blood:
9	chr4:15680881..15687102-chr4:15687861..15693031,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000237765	Chromatin interaction
ENSG00000118564	Chromatin interaction
ENSG00000137440	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10005305	0.89[AFR][1000 genomes]
rs10008878	0.87[AFR][1000 genomes]
rs10009089	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10017222	1.00[CHB][hapmap]
rs10025875	0.88[AFR][1000 genomes]
rs10034315	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10516289	1.00[CHB][hapmap]
rs11722757	0.98[ASN][1000 genomes]
rs11722854	0.81[ASN][1000 genomes]
rs11723478	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11723554	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs11726647	0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11729955	1.00[CHB][hapmap]
rs11732953	0.83[AFR][1000 genomes]
rs11735063	1.00[CHB][hapmap]
rs12642407	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650529	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13106528	0.86[JPT][hapmap]
rs13131119	0.86[JPT][hapmap]
rs13134177	0.82[AFR][1000 genomes]
rs13141724	0.82[JPT][hapmap]
rs13144428	0.86[JPT][hapmap]
rs13150957	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1468735	0.86[JPT][hapmap]
rs16892135	0.86[JPT][hapmap]
rs16892143	0.86[JPT][hapmap]
rs17405811	1.00[CHB][hapmap]
rs17476642	1.00[CHB][hapmap]
rs17476670	0.86[JPT][hapmap]
rs1786	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.82[MEX][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2041672	0.86[JPT][hapmap]
rs2041673	0.86[JPT][hapmap]
rs28394730	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28402170	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28447067	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28604503	0.81[ASN][1000 genomes]
rs28644177	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28820655	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34473224	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34559117	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34831330	0.86[JPT][hapmap]
rs34955342	0.98[ASN][1000 genomes]
rs35013326	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35120298	0.96[ASN][1000 genomes]
rs3756247	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775956	0.89[AFR][1000 genomes]
rs3775957	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs41417147	0.86[JPT][hapmap]
rs4257653	0.98[ASN][1000 genomes]
rs4267734	0.87[ASW][hapmap];0.86[JPT][hapmap]
rs4301111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4326008	0.86[JPT][hapmap]
rs4331772	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4346644	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4396986	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423870	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4484296	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4554069	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4600905	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4698116	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6414764	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]
rs6449150	0.81[ASW][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.84[YRI][hapmap]
rs6815296	1.00[CHB][hapmap]
rs6816982	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823775	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6824422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6825051	0.86[JPT][hapmap];0.89[YRI][hapmap]
rs6825815	0.86[JPT][hapmap]
rs6826058	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6827406	1.00[CHB][hapmap]
rs6828776	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6835038	0.86[JPT][hapmap]
rs6839654	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843740	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844141	0.86[JPT][hapmap]
rs6848779	0.88[ASW][hapmap];1.00[CHB][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs6852735	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6857442	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7434484	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7667175	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698596	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994518	0.88[ASW][hapmap];0.85[CHB][hapmap];0.98[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6815254	FAM200B,LOC285550	cis	temporal cortex	BrainEAC
rs6815254	LOC285550	cis	lesional skin	skin_eQTL
rs6815254	LOC285550	cis	normal skin	skin_eQTL
rs6815254	FAM200B	cis	cerebellum	SCAN
rs6815254	LOC285550	cis	uninvolved skin	skin_eQTL
rs6815254	FAM200B,LOC285550	cis	brain	BrainEAC
rs6815254	FAM200B	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15684000-15692400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:15684000-15697000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:15684000-15704400	Weak transcription	Left Ventricle	heart
4	chr4:15684400-15692200	Weak transcription	Right Ventricle	heart
5	chr4:15684800-15692200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:15684800-15692400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:15684800-15693600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:15684800-15694200	Weak transcription	Fetal Brain Male	brain
9	chr4:15684800-15704400	Weak transcription	Aorta	Aorta
10	chr4:15685000-15693000	Weak transcription	Psoas Muscle	Psoas
11	chr4:15685000-15695800	Weak transcription	Stomach Mucosa	stomach
12	chr4:15686000-15692200	Weak transcription	Brain Angular Gyrus	brain
13	chr4:15686000-15692400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:15686400-15692200	Weak transcription	Small Intestine	intestine
15	chr4:15686400-15692800	Weak transcription	GM12878-XiMat	blood
16	chr4:15686600-15704400	Weak transcription	Thymus	Thymus
17	chr4:15687000-15692200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:15687200-15701200	Weak transcription	Fetal Intestine Small	intestine
19	chr4:15687600-15692200	Weak transcription	Ovary	ovary
20	chr4:15687600-15696800	Weak transcription	Fetal Stomach	stomach
21	chr4:15687600-15697000	Weak transcription	Esophagus	oesophagus
22	chr4:15688400-15692200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:15688400-15692200	Weak transcription	Fetal Muscle Leg	muscle
24	chr4:15688400-15692400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:15688400-15697200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:15688400-15703800	Weak transcription	Fetal Kidney	kidney
27	chr4:15688600-15692200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:15688600-15692200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:15688600-15695600	Weak transcription	Fetal Lung	lung
30	chr4:15689400-15692800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:15689400-15693000	Weak transcription	K562	blood
32	chr4:15689400-15693600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:15689600-15692600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:15689600-15692800	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:15689600-15697200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr4:15690000-15692800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr4:15690000-15693000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr4:15690000-15693400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:15690200-15695000	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr4:15690400-15694200	Enhancers	Adipose Nuclei	Adipose
41	chr4:15690600-15692200	Strong transcription	Brain Germinal Matrix	brain
42	chr4:15690600-15693600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr4:15690600-15694600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:15690600-15697800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:15690800-15693200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:15690800-15693600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr4:15690800-15693800	Enhancers	HSMMtube	muscle
48	chr4:15690800-15694000	Enhancers	HMEC	breast
49	chr4:15690800-15694000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr4:15691000-15692200	Enhancers	NHDF-Ad	bronchial

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