Variant report

Variant	rs6603046
Chromosome Location	chr15:83733001-83733002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:83732868-83733068	MCF10A-Er-Src	breast:	n/a	n/a
2	FOXA1	chr15:83732648-83733103	HepG2	liver:	n/a	n/a
3	CHD1	chr15:83732419-83733082	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:83732977-83733027	A549	lung:	n/a
2	chr15:83732977-83733027	GM19239	blood:	n/a
3	chr15:83732977-83733027	T-47D	breast:	n/a
4	chr15:83732977-83733027	ECC-1	luminal epithelium:	n/a
5	chr15:83732977-83733027	HRCEpiC	kidney:	n/a
6	chr15:83732977-83733027	BE2_C	brain:	n/a
7	chr15:83732977-83733027	AG04449	skin:	fetal
8	chr15:83732977-83733027	GM12878	blood:	n/a
9	chr15:83732977-83733027	AG10803	skin:	n/a
10	chr15:83732977-83733027	NH-A	brain:	n/a
11	chr15:83732977-83733027	HRPEpiC	eye:	n/a
12	chr15:83732977-83733027	ovcar-3	ovarian:	n/a
13	chr15:83732977-83733027	PANC-1	pancreas:	n/a
14	chr15:83732977-83733027	HUVEC	blood vessel:	n/a
15	chr15:83732977-83733027	LNCaP	prostate:	n/a
16	chr15:83732977-83733027	U87	brain:	n/a
17	chr15:83732977-83733027	HEK293	kidney:	embryo
18	chr15:83732977-83733027	NHBE	bronchial:	n/a
19	chr15:83732977-83733027	GM12892	blood:	n/a
20	chr15:83732977-83733027	HAEpiC	amniotic membrane:	n/a
21	chr15:83732977-83733027	BJ	skin:	n/a
22	chr15:83732977-83733027	SAEC	small airway:	n/a
23	chr15:83732977-83733027	SKMC	muscle:	n/a
24	chr15:83732977-83733027	HNPCEpiC	eye:	n/a
25	chr15:83732977-83733027	CMK	blood:	n/a
26	chr15:83732977-83733027	AG09319	gingival:	n/a
27	chr15:83732977-83733027	NT2-D1	testis:	n/a
28	chr15:83732977-83733027	PFSK-1	brain:	n/a
29	chr15:83732977-83733027	HPAEpiC	pulmonary alveolar:	n/a
30	chr15:83732977-83733027	Hepatocyte	liver:	n/a
31	chr15:83732977-83733027	SK-N-SH	brain:	n/a
32	chr15:83732977-83733027	HIPEpiC	eye:	n/a
33	chr15:83732977-83733027	MCF-7	breast:	n/a
34	chr15:83732977-83733027	MCF10A-Er-Src	breast:	n/a
35	chr15:83732977-83733027	RPTEC	kidney:	n/a
36	chr15:83732977-83733027	HL-60	blood:	n/a
37	chr15:83732977-83733027	AG09309	skin:	n/a
38	chr15:83732977-83733027	HCM	heart:	n/a
39	chr15:83732977-83733027	AG04450	lung:	fetal
40	chr15:83732977-83733027	SK-N-MC	brain:	n/a
41	chr15:83732977-83733027	HCT-116	colon:	n/a
42	chr15:83732977-83733027	Hela-S3	cervix:	n/a
43	chr15:83732977-83733027	K562	blood:	n/a
44	chr15:83732977-83733027	AoSMC	blood vessel:	n/a
45	chr15:83732977-83733027	HEEpiC	esophagus:	n/a
46	chr15:83732977-83733027	ProgFib	skin:	n/a
47	chr15:83732977-83733027	HCPEpiC	choroid plexus:	n/a
48	chr15:83732977-83733027	HMEC	breast:	n/a
49	chr15:83732977-83733027	Caco-2	colon:	n/a
50	chr15:83732977-83733027	H1-hESC	embryonic stem cell:	embryo

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83731812..83734557-chr15:83779300..83781603,2	K562	blood:
2	chr15:83731597..83733355-chr15:83864514..83866246,2	K562	blood:
3	chr15:83732514..83734789-chr15:83841378..83843328,2	MCF-7	breast:
4	chr15:83731060..83733792-chr15:83908261..83911046,2	K562	blood:
5	chr15:83716790..83719307-chr15:83732798..83735567,2	MCF-7	breast:
6	chr15:83678535..83684480-chr15:83731660..83738533,12	MCF-7	breast:
7	chr15:83684703..83687598-chr15:83730655..83733296,2	K562	blood:
8	chr15:83731075..83738271-chr15:83771545..83781798,12	K562	blood:
9	chr15:83728223..83733279-chr15:83872338..83876797,5	MCF-7	breast:
10	chr15:83731888..83734386-chr15:83806959..83808488,2	K562	blood:
11	chr15:83730196..83733187-chr15:83768723..83771408,2	K562	blood:
12	chr15:83684589..83686265-chr15:83730370..83733896,3	K562	blood:

No data

Variant related genes	Relation type
MIR4515	TF binding region
MIR4515	CpG island
ENSG00000169609	Chromatin interaction
ENSG00000136404	Chromatin interaction
ENSG00000249214	Chromatin interaction
ENSG00000260608	Chromatin interaction
ENSG00000166503	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10400812	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10520576	1.00[JPT][hapmap]
rs1112404	1.00[JPT][hapmap]
rs11259965	1.00[JPT][hapmap]
rs11259969	1.00[JPT][hapmap]
rs11852408	1.00[JPT][hapmap]
rs11852496	1.00[JPT][hapmap]
rs11853742	0.91[JPT][hapmap]
rs11856171	1.00[JPT][hapmap]
rs11857428	1.00[JPT][hapmap]
rs11857641	1.00[JPT][hapmap]
rs11858074	0.94[ASN][1000 genomes]
rs11858377	1.00[JPT][hapmap]
rs12439782	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12440386	1.00[JPT][hapmap]
rs12441585	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12443109	1.00[JPT][hapmap]
rs12591855	1.00[JPT][hapmap]
rs12592391	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12593316	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12593638	0.91[JPT][hapmap]
rs12594496	1.00[JPT][hapmap]
rs12595330	1.00[JPT][hapmap]
rs12899522	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12900411	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12901811	0.94[ASN][1000 genomes]
rs12902721	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12903066	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12904695	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12906027	0.94[ASN][1000 genomes]
rs12906626	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12907032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911706	0.94[ASN][1000 genomes]
rs12911891	0.94[ASN][1000 genomes]
rs12913130	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12917594	0.95[ASN][1000 genomes]
rs13329195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13329269	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17158080	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs17158127	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17294476	0.90[JPT][hapmap]
rs17507300	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17567151	1.00[JPT][hapmap]
rs17567869	1.00[JPT][hapmap]
rs17568459	1.00[JPT][hapmap]
rs2034617	0.91[JPT][hapmap]
rs2034618	1.00[JPT][hapmap]
rs2084839	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2381030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28436027	0.91[JPT][hapmap]
rs28485801	0.95[ASN][1000 genomes]
rs28580677	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3087804	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34869943	0.90[ASN][1000 genomes]
rs35207081	0.94[ASN][1000 genomes]
rs35627116	0.95[ASN][1000 genomes]
rs36038412	0.94[ASN][1000 genomes]
rs4079029	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4563011	1.00[JPT][hapmap]
rs61375537	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6603044	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6603047	0.91[JPT][hapmap]
rs66606849	0.94[ASN][1000 genomes]
rs67482297	0.94[ASN][1000 genomes]
rs67822554	0.94[ASN][1000 genomes]
rs7163516	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7164083	0.82[JPT][hapmap]
rs7165114	1.00[JPT][hapmap]
rs7165978	1.00[JPT][hapmap]
rs7166645	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170547	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172665	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7177599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7180407	1.00[JPT][hapmap]
rs7181169	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7495911	1.00[JPT][hapmap]
rs750214	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8023669	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs8027193	1.00[JPT][hapmap]
rs8027577	1.00[JPT][hapmap]
rs8031896	0.97[ASN][1000 genomes]
rs8035810	1.00[JPT][hapmap]
rs8037783	1.00[JPT][hapmap]
rs8038486	1.00[JPT][hapmap]
rs8040457	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8043224	1.00[JPT][hapmap]
rs9646239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs965264	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6603046	WHAMM	cis	parietal	SCAN
rs6603046	BTBD1	cis	parietal	SCAN
rs6603046	WHAMM	cis	cerebellum	SCAN
rs6603046	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL
rs6603046	TM6SF1	cis	cerebellum	SCAN
rs6603046	ARNT2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83700400-83734400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:83725000-83733800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:83725400-83734600	Weak transcription	Placenta	Placenta
4	chr15:83725600-83734400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:83726800-83733600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:83727400-83734200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:83729400-83733200	Enhancers	Fetal Intestine Large	intestine
8	chr15:83729600-83733800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:83729600-83733800	Enhancers	Fetal Kidney	kidney
10	chr15:83729800-83733600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr15:83729800-83733600	Enhancers	Fetal Heart	heart
12	chr15:83729800-83733800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr15:83729800-83734400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr15:83730000-83733400	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr15:83730200-83733200	Enhancers	NH-A	brain
16	chr15:83730200-83733400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr15:83730200-83733600	Enhancers	NHDF-Ad	bronchial
18	chr15:83730200-83734600	Enhancers	Small Intestine	intestine
19	chr15:83730400-83733200	Enhancers	Fetal Intestine Small	intestine
20	chr15:83730400-83734400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr15:83730400-83734600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:83730600-83733400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:83730600-83733600	Enhancers	Adipose Nuclei	Adipose
24	chr15:83730600-83734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:83730600-83734400	Weak transcription	Esophagus	oesophagus
26	chr15:83730600-83734400	Weak transcription	Lung	lung
27	chr15:83731000-83733200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:83731000-83733600	Weak transcription	HSMMtube	muscle
29	chr15:83731000-83734200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr15:83731200-83733400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:83731200-83734400	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr15:83731400-83733200	Transcr. at gene 5' and 3'	K562	blood
33	chr15:83731400-83733400	Enhancers	Brain Germinal Matrix	brain
34	chr15:83731400-83733800	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr15:83731400-83733800	Enhancers	Brain Substantia Nigra	brain
36	chr15:83731400-83734400	Enhancers	Primary B cells from peripheral blood	blood
37	chr15:83731400-83736800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:83731600-83733200	Enhancers	Primary T cells from cord blood	blood
39	chr15:83731600-83733400	Enhancers	Primary hematopoietic stem cells	blood
40	chr15:83731600-83733400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:83731600-83733800	Weak transcription	Colonic Mucosa	Colon
42	chr15:83731600-83734600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr15:83731800-83733400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:83731800-83733400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:83731800-83733600	Enhancers	Liver	Liver
46	chr15:83732000-83733200	Enhancers	Stomach Mucosa	stomach
47	chr15:83732200-83733400	Enhancers	H1 Cell Line	embryonic stem cell
48	chr15:83732200-83734200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr15:83732200-83734600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr15:83732400-83733200	Enhancers	Primary B cells from cord blood	blood

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