Variant report

Variant	rs646924
Chromosome Location	chr11:59950417-59950418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr11:59950069-59950446	MCF10A-Er-Src	breast:	n/a	chr11:59950252-59950262 chr11:59950252-59950262 chr11:59950252-59950262
2	FOS	chr11:59950073-59950435	MCF10A-Er-Src	breast:	n/a	chr11:59950252-59950262 chr11:59950252-59950262 chr11:59950252-59950262
3	FOS	chr11:59950075-59950440	MCF10A-Er-Src	breast:	n/a	chr11:59950252-59950262 chr11:59950252-59950262 chr11:59950252-59950262
4	MYC	chr11:59950257-59950457	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr11:59950067-59950436	MCF10A-Er-Src	breast:	n/a	chr11:59950252-59950262 chr11:59950252-59950262 chr11:59950252-59950262
6	SPI1	chr11:59950409-59950817	HL-60	blood:	n/a	chr11:59950635-59950648
7	SPI1	chr11:59950304-59950880	HL-60	blood:	n/a	chr11:59950635-59950648

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:59950405-59950455	NH-A	brain:	n/a
2	chr11:59950405-59950455	H1-hESC	embryonic stem cell:	embryo
3	chr11:59950405-59950455	HIPEpiC	eye:	n/a
4	chr11:59950405-59950455	Hepatocyte	liver:	n/a
5	chr11:59950405-59950455	PANC-1	pancreas:	n/a
6	chr11:59950405-59950455	HEK293	kidney:	embryo
7	chr11:59950405-59950455	MCF10A-Er-Src	breast:	n/a
8	chr11:59950405-59950455	IMR90	lung:	fetal
9	chr11:59950405-59950455	BJ	skin:	n/a
10	chr11:59950405-59950455	AG09309	skin:	n/a
11	chr11:59950405-59950455	CMK	blood:	n/a
12	chr11:59950405-59950455	GM12878	blood:	n/a
13	chr11:59950405-59950455	HPAEpiC	pulmonary alveolar:	n/a
14	chr11:59950405-59950455	A549	lung:	n/a
15	chr11:59950405-59950455	AG04449	skin:	fetal
16	chr11:59950405-59950455	GM06990	blood:	n/a
17	chr11:59950405-59950455	HCM	heart:	n/a
18	chr11:59950405-59950455	HRPEpiC	eye:	n/a
19	chr11:59950405-59950455	MCF-7	breast:	n/a
20	chr11:59950405-59950455	SAEC	small airway:	n/a
21	chr11:59950405-59950455	RPTEC	kidney:	n/a
22	chr11:59950405-59950455	HNPCEpiC	eye:	n/a
23	chr11:59950405-59950455	HCF	heart:	n/a
24	chr11:59950405-59950455	HCT-116	colon:	n/a
25	chr11:59950405-59950455	GM12891	blood:	n/a
26	chr11:59950405-59950455	SK-N-SH_RA	brain:	n/a
27	chr11:59950405-59950455	HMEC	breast:	n/a
28	chr11:59950405-59950455	ECC-1	luminal epithelium:	n/a
29	chr11:59950405-59950455	BE2_C	brain:	n/a
30	chr11:59950405-59950455	PrEC	prostate:	n/a
31	chr11:59950405-59950455	GM19239	blood:	n/a
32	chr11:59950405-59950455	HRCEpiC	kidney:	n/a
33	chr11:59950405-59950455	SK-N-SH	brain:	n/a
34	chr11:59950405-59950455	AG09319	gingival:	n/a
35	chr11:59950405-59950455	ProgFib	skin:	n/a
36	chr11:59950405-59950455	NHDF-neo	bronchial:	n/a
37	chr11:59950405-59950455	HepG2	liver:	n/a
38	chr11:59950405-59950455	T-47D	breast:	n/a
39	chr11:59950405-59950455	NHBE	bronchial:	n/a
40	chr11:59950405-59950455	SKMC	muscle:	n/a
41	chr11:59950405-59950455	PFSK-1	brain:	n/a
42	chr11:59950405-59950455	Hela-S3	cervix:	n/a
43	chr11:59950405-59950455	LNCaP	prostate:	n/a
44	chr11:59950405-59950455	U87	brain:	n/a
45	chr11:59950405-59950455	Jurkat	blood:	n/a
46	chr11:59950405-59950455	HUVEC	blood vessel:	n/a
47	chr11:59950405-59950455	NT2-D1	testis:	n/a
48	chr11:59950405-59950455	NB4	blood:	n/a
49	chr11:59950405-59950455	HAEpiC	amniotic membrane:	n/a
50	chr11:59950405-59950455	HL-60	blood:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MS4A4E-1	chr11:59950278-59950804	NONHSAT021563

No data

Variant related genes	Relation type
MS4A6A	TF binding region
MS4A6A	CpG island

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10750930	0.89[JPT][hapmap]
rs1286182	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1294440	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs1303617	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1303618	0.96[EUR][1000 genomes]
rs1303619	0.96[EUR][1000 genomes]
rs1303620	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1303622	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1315507	0.96[EUR][1000 genomes]
rs1426252	0.87[ASN][1000 genomes]
rs1441585	0.90[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs2081546	0.87[ASN][1000 genomes]
rs2243987	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433240	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847662	0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs474888	0.96[EUR][1000 genomes]
rs475494	0.96[EUR][1000 genomes]
rs475812	0.89[JPT][hapmap];0.96[EUR][1000 genomes]
rs477352	0.96[EUR][1000 genomes]
rs485682	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs489297	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs500886	0.96[EUR][1000 genomes]
rs500888	0.96[EUR][1000 genomes]
rs512548	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs512555	0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs519743	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs523806	0.96[EUR][1000 genomes]
rs524755	0.96[EUR][1000 genomes]
rs524995	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs528421	0.96[EUR][1000 genomes]
rs535413	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs541468	0.96[EUR][1000 genomes]
rs542665	0.96[EUR][1000 genomes]
rs546840	0.96[EUR][1000 genomes]
rs548515	0.96[EUR][1000 genomes]
rs549633	0.96[EUR][1000 genomes]
rs562442	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs562637	0.96[EUR][1000 genomes]
rs569108	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs571582	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs572084	0.96[EUR][1000 genomes]
rs573305	0.96[EUR][1000 genomes]
rs574060	0.96[EUR][1000 genomes]
rs574700	0.82[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs575103	0.96[EUR][1000 genomes]
rs575930	0.96[EUR][1000 genomes]
rs576295	0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs576483	0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs576616	0.96[EUR][1000 genomes]
rs578269	0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs581818	1.00[ASN][1000 genomes]
rs582407	0.87[ASN][1000 genomes]
rs585540	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs587634	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588448	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs590351	0.97[ASN][1000 genomes]
rs590532	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs592496	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594414	0.87[ASN][1000 genomes]
rs595014	0.87[ASN][1000 genomes]
rs596788	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597982	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs598862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600194	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs605820	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs607639	0.87[ASN][1000 genomes]
rs613548	0.84[ASN][1000 genomes]
rs613629	0.87[ASN][1000 genomes]
rs615405	0.87[ASN][1000 genomes]
rs620368	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs624233	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625025	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636988	0.87[ASN][1000 genomes]
rs638872	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641051	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs642426	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649234	0.86[ASN][1000 genomes]
rs650777	0.87[ASN][1000 genomes]
rs650853	0.85[ASN][1000 genomes]
rs650926	0.87[ASN][1000 genomes]
rs653285	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654443	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661376	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs662674	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs668095	0.92[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs668134	0.92[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs670925	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672218	0.87[ASN][1000 genomes]
rs674971	0.87[ASN][1000 genomes]
rs675316	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675452	0.84[ASN][1000 genomes]
rs680699	0.97[ASN][1000 genomes]
rs682025	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs682739	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684977	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73485360	0.81[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	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv832174	chr11:59909267-60073908	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs646924	MS4A6A	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59946800-59952000	Active TSS	Adipose Nuclei	Adipose
2	chr11:59947600-59953000	Enhancers	Fetal Intestine Small	intestine
3	chr11:59947800-59950600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:59948600-59950600	Active TSS	Liver	Liver
5	chr11:59948600-59950600	Active TSS	Fetal Muscle Leg	muscle
6	chr11:59948800-59951000	Active TSS	Primary monocytes fromperipheralblood	blood
7	chr11:59949000-59950600	Active TSS	Brain Anterior Caudate	brain
8	chr11:59949000-59950600	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr11:59949000-59950600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr11:59949200-59950600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr11:59949200-59950600	Active TSS	Monocytes-CD14+_RO01746	blood
12	chr11:59949800-59950600	Active TSS	Right Atrium	heart
13	chr11:59949800-59951000	Enhancers	Dnd41	blood
14	chr11:59949800-59952000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:59950000-59950600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:59950000-59950600	Active TSS	Duodenum Mucosa	Duodenum
17	chr11:59950000-59950800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:59950000-59951600	Enhancers	HUVEC	blood vessel
19	chr11:59950000-59954800	Enhancers	Primary B cells from peripheral blood	blood
20	chr11:59950200-59950600	Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr11:59950200-59950600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:59950200-59950800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr11:59950200-59951000	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr11:59950200-59951400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:59950200-59951400	Weak transcription	Spleen	Spleen
26	chr11:59950400-59950600	Enhancers	GM12878-XiMat	blood
27	chr11:59950400-59950600	Enhancers	K562	blood
28	chr11:59950400-59952600	Enhancers	Primary hematopoietic stem cells	blood
29	chr11:59950400-59954600	Enhancers	Fetal Intestine Large	intestine

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