Variant report

Variant	rs12669568
Chromosome Location	chr7:107885943-107885944
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:107885906-107885956	AG04450	lung:	fetal
2	chr7:107885906-107885956	SKMC	muscle:	n/a
3	chr7:107885906-107885956	SK-N-MC	brain:	n/a
4	chr7:107885906-107885956	CMK	blood:	n/a
5	chr7:107885906-107885956	U87	brain:	n/a
6	chr7:107885906-107885956	NH-A	brain:	n/a
7	chr7:107885906-107885956	HAEpiC	amniotic membrane:	n/a
8	chr7:107885906-107885956	T-47D	breast:	n/a
9	chr7:107885906-107885956	RPTEC	kidney:	n/a
10	chr7:107885906-107885956	PFSK-1	brain:	n/a
11	chr7:107885906-107885956	Hepatocyte	liver:	n/a
12	chr7:107885906-107885956	H1-hESC	embryonic stem cell:	embryo
13	chr7:107885906-107885956	PANC-1	pancreas:	n/a
14	chr7:107885906-107885956	AoSMC	blood vessel:	n/a
15	chr7:107885906-107885956	SK-N-SH	brain:	n/a
16	chr7:107885906-107885956	SAEC	small airway:	n/a
17	chr7:107885906-107885956	NT2-D1	testis:	n/a
18	chr7:107885906-107885956	HCPEpiC	choroid plexus:	n/a
19	chr7:107885906-107885956	MCF10A-Er-Src	breast:	n/a
20	chr7:107885906-107885956	Caco-2	colon:	n/a
21	chr7:107885906-107885956	HCT-116	colon:	n/a
22	chr7:107885906-107885956	ECC-1	luminal epithelium:	n/a
23	chr7:107885906-107885956	HPAEpiC	pulmonary alveolar:	n/a
24	chr7:107885906-107885956	HIPEpiC	eye:	n/a
25	chr7:107885906-107885956	GM12892	blood:	n/a
26	chr7:107885906-107885956	HCM	heart:	n/a
27	chr7:107885906-107885956	AG09319	gingival:	n/a
28	chr7:107885906-107885956	LNCaP	prostate:	n/a
29	chr7:107885906-107885956	SK-N-SH_RA	brain:	n/a
30	chr7:107885906-107885956	GM19239	blood:	n/a
31	chr7:107885906-107885956	HCF	heart:	n/a
32	chr7:107885906-107885956	BE2_C	brain:	n/a
33	chr7:107885906-107885956	GM12891	blood:	n/a
34	chr7:107885906-107885956	ProgFib	skin:	n/a
35	chr7:107885906-107885956	GM12878	blood:	n/a
36	chr7:107885906-107885956	BJ	skin:	n/a
37	chr7:107885906-107885956	HNPCEpiC	eye:	n/a
38	chr7:107885906-107885956	HRPEpiC	eye:	n/a
39	chr7:107885906-107885956	Jurkat	blood:	n/a
40	chr7:107885906-107885956	NHDF-neo	bronchial:	n/a
41	chr7:107885906-107885956	HepG2	liver:	n/a
42	chr7:107885906-107885956	IMR90	lung:	fetal
43	chr7:107885906-107885956	AG10803	skin:	n/a
44	chr7:107885906-107885956	HEK293	kidney:	embryo
45	chr7:107885906-107885956	NHBE	bronchial:	n/a
46	chr7:107885906-107885956	HUVEC	blood vessel:	n/a
47	chr7:107885906-107885956	PrEC	prostate:	n/a
48	chr7:107885906-107885956	HEEpiC	esophagus:	n/a
49	chr7:107885906-107885956	HRCEpiC	kidney:	n/a
50	chr7:107885906-107885956	MCF-7	breast:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr7:107885403..107887866-chr7:108208741..108211380,3	K562	blood:
2	chr7:107885138..107886888-chr7:108093240..108094894,2	K562	blood:
3	chr7:107844217..107846862-chr7:107884511..107886903,2	K562	blood:
4	chr7:107880432..107884512-chr7:107884667..107887859,3	MCF-7	breast:
5	chr7:107885764..107888071-chr7:107990459..107993788,3	MCF-7	breast:
6	chr7:107883815..107886718-chr7:108095136..108097625,2	MCF-7	breast:
7	chr7:107885444..107889446-chr7:107936320..107941216,4	MCF-7	breast:

No data

Variant related genes	Relation type
NRCAM	CpG island
ENSG00000177683	Chromatin interaction
ENSG00000128590	Chromatin interaction
ENSG00000091129	Chromatin interaction
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10224607	1.00[CEU][hapmap]
rs10257555	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs10464622	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10464623	0.95[EUR][1000 genomes]
rs10464625	0.95[EUR][1000 genomes]
rs10464626	0.95[EUR][1000 genomes]
rs10464627	0.90[EUR][1000 genomes]
rs10464628	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12531903	1.00[CEU][hapmap]
rs12665964	0.91[EUR][1000 genomes]
rs12667098	0.95[EUR][1000 genomes]
rs12667131	0.95[EUR][1000 genomes]
rs12667151	0.95[EUR][1000 genomes]
rs12667206	0.95[EUR][1000 genomes]
rs12671199	0.85[EUR][1000 genomes]
rs12672376	0.90[EUR][1000 genomes]
rs12674151	0.95[EUR][1000 genomes]
rs12674313	0.81[EUR][1000 genomes]
rs16872446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16872448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16872449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16872465	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872472	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16872481	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs17155207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17155253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17155277	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17155280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17155301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17155316	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17155345	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17155362	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17155369	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2072320	1.00[EUR][1000 genomes]
rs2272618	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2284279	1.00[CEU][hapmap]
rs2284281	1.00[CEU][hapmap]
rs2299988	1.00[CEU][hapmap]
rs2299998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2300001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2300004	1.00[EUR][1000 genomes]
rs2300005	1.00[EUR][1000 genomes]
rs2300006	1.00[EUR][1000 genomes]
rs2300007	0.95[EUR][1000 genomes]
rs2300008	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2300009	0.95[EUR][1000 genomes]
rs2300010	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2300011	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs369800	0.82[CHD][hapmap]
rs3750140	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3753152	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3801929	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs3817670	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs404287	0.82[CHD][hapmap]
rs404453	0.82[ASW][hapmap];0.82[CHD][hapmap]
rs425013	0.82[CHD][hapmap]
rs55772998	1.00[EUR][1000 genomes]
rs58432175	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58523350	1.00[EUR][1000 genomes]
rs58799340	1.00[EUR][1000 genomes]
rs59173255	1.00[EUR][1000 genomes]
rs60503554	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61040788	1.00[EUR][1000 genomes]
rs61057696	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67456250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67592649	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67940074	0.95[EUR][1000 genomes]
rs6956041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6956711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6964394	1.00[EUR][1000 genomes]
rs6966259	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];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6970634	0.86[EUR][1000 genomes]
rs6978117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73199578	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73199594	0.95[EUR][1000 genomes]
rs73199595	0.95[EUR][1000 genomes]
rs73199599	0.95[EUR][1000 genomes]
rs73199600	0.95[EUR][1000 genomes]
rs73201503	1.00[EUR][1000 genomes]
rs73201504	1.00[EUR][1000 genomes]
rs73201511	1.00[EUR][1000 genomes]
rs73201512	1.00[EUR][1000 genomes]
rs73201513	1.00[EUR][1000 genomes]
rs73201515	1.00[EUR][1000 genomes]
rs73414373	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73727511	0.95[EUR][1000 genomes]
rs73727512	0.95[EUR][1000 genomes]
rs7777092	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7777322	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7783944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7784319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7784353	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7785181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7796457	1.00[EUR][1000 genomes]
rs9641405	1.00[EUR][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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12669568	CCL3	trans	brain	seeQTL
rs12669568	EGR2	trans	brain	seeQTL
rs12669568	PTGS2	trans	brain	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107830400-107886400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr7:107860600-107886600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:107871200-107886400	Weak transcription	Brain Anterior Caudate	brain
4	chr7:107874800-107886200	Weak transcription	HSMMtube	muscle
5	chr7:107876400-107886400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:107877000-107886200	Weak transcription	HMEC	breast
7	chr7:107877800-107886400	Weak transcription	Pancreas	Pancrea
8	chr7:107880400-107886200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:107880600-107887000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:107880800-107886600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:107881000-107886200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:107881200-107886000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:107881200-107886400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:107881200-107886400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:107881200-107886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:107881200-107886400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:107881200-107886600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr7:107881800-107886400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:107883600-107886800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:107884400-107886200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:107884400-107886200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:107884600-107886000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:107884600-107886200	Enhancers	NHDF-Ad	bronchial
24	chr7:107884800-107886400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr7:107884800-107886400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:107884800-107886400	Weak transcription	Fetal Intestine Small	intestine
27	chr7:107884800-107890600	Weak transcription	Brain Substantia Nigra	brain
28	chr7:107885000-107886000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:107885200-107886400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr7:107885200-107886400	Enhancers	K562	blood
31	chr7:107885400-107886400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:107885400-107886400	Weak transcription	Fetal Intestine Large	intestine
33	chr7:107885600-107886000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr7:107885600-107887000	Enhancers	HSMM	muscle
35	chr7:107885600-107888400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr7:107885600-107889400	Enhancers	Osteobl	bone
37	chr7:107885800-107886400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr7:107885800-107887600	Flanking Active TSS	A549	lung
39	chr7:107885800-107887600	Enhancers	NHLF	lung
40	chr7:107885800-107888400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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