Variant report

Variant	rs6768844
Chromosome Location	chr3:53004620-53004621
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	chr3:53004365..53006043-chr3:53009863..53012220,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 19 )

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

rs_ID	r²[population]
rs11130332	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1134546	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11706243	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11707576	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11708223	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072536	0.80[CEU][hapmap]
rs13082061	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13083728	0.82[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs1573815	0.82[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs17304995	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2245424	0.91[JPT][hapmap]
rs2246556	0.84[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255107	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2257216	0.91[JPT][hapmap]
rs2276817	0.82[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs2276825	0.94[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap]
rs2336162	0.90[EUR][1000 genomes]
rs2336666	0.83[EUR][1000 genomes]
rs2336669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2336670	0.90[JPT][hapmap]
rs2336671	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2564947	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2581779	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2581780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2581796	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2581797	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2581801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2581802	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2581803	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2581805	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2581810	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2581815	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2581820	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2581823	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2710314	0.91[JPT][hapmap]
rs2710342	0.84[EUR][1000 genomes]
rs2710345	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34230854	0.89[EUR][1000 genomes]
rs35380116	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3733047	0.82[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4302374	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs4519686	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687554	0.82[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4687559	0.84[EUR][1000 genomes]
rs4687560	0.84[EUR][1000 genomes]
rs4687658	0.82[CEU][hapmap]
rs4687663	0.82[CEU][hapmap]
rs4687672	0.81[CEU][hapmap]
rs4687692	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687699	0.80[EUR][1000 genomes]
rs59989280	0.88[EUR][1000 genomes]
rs6445538	0.82[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs6445539	0.82[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs6445547	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs6445550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770957	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6771610	0.84[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6773040	0.84[EUR][1000 genomes]
rs6789219	0.88[EUR][1000 genomes]
rs6792578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs6797399	0.82[EUR][1000 genomes]
rs6803519	0.82[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs6805298	0.88[EUR][1000 genomes]
rs71301803	0.89[EUR][1000 genomes]
rs71301807	0.90[EUR][1000 genomes]
rs7621939	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7637082	0.82[EUR][1000 genomes]
rs7644973	0.90[EUR][1000 genomes]
rs7648514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7652131	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9311485	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9682464	0.94[CEU][hapmap]
rs9812543	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9813024	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9823697	0.91[JPT][hapmap]
rs9825679	0.88[ASN][1000 genomes]
rs9828491	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9831409	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9839035	0.82[EUR][1000 genomes]
rs9842974	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9844736	0.93[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.88[LWK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs9846976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847024	0.92[EUR][1000 genomes]
rs9865094	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9870898	1.00[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs9876403	0.94[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.86[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	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv3823	chr3:53003659-53051063	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs6768844	GNL3	cis	cerebellum	SCAN
rs6768844	RBM6	cis	cerebellum	SCAN
rs6768844	AMT	cis	parietal	SCAN
rs6768844	ITIH4	cis	lymphoblastoid	seeQTL
rs6768844	SERBP1P3	cis	lung	GTEx
rs6768844	ITIH4	cis	cerebellum	SCAN
rs6768844	ITIH4	cis	parietal	SCAN
rs6768844	NT5DC2	cis	parietal	SCAN
rs6768844	SEMA3G	cis	parietal	SCAN
rs6768844	WDR6	cis	cerebellum	SCAN
rs6768844	ITIH4-AS1	cis	Artery Tibial	GTEx
rs6768844	RFT1	cis	cerebellum	SCAN
rs6768844	ITIH4	cis	multi-tissue	Pritchard
rs6768844	ITIH4-AS1	cis	Artery Aorta	GTEx
rs6768844	ITIH4-AS1	cis	lung	GTEx
rs6768844	MUSTN1	cis	Artery Aorta	GTEx
rs6768844	GNL3	cis	parietal	SCAN
rs6768844	TMEM110	cis	cerebellum	SCAN
rs6768844	TMEM110	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus
2	chr3:52954200-53012200	Weak transcription	Pancreas	Pancrea
3	chr3:52962400-53007000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:52962400-53012400	Weak transcription	Adipose Nuclei	Adipose
5	chr3:52964600-53012200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
7	chr3:52965600-53008200	Weak transcription	GM12878-XiMat	blood
8	chr3:52969000-53008000	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:52975000-53008000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:52977600-53017000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:52984400-53006000	Weak transcription	Fetal Heart	heart
12	chr3:52986400-53012200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:52986800-53006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:52987200-53017400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:52987600-53005800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:52987600-53009400	Weak transcription	Placenta	Placenta
17	chr3:52987600-53014200	Weak transcription	Fetal Thymus	thymus
18	chr3:52987600-53014200	Weak transcription	Thymus	Thymus
19	chr3:52987800-53017000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:52987800-53017000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr3:52988000-53004800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:52988000-53014200	Weak transcription	Primary T cells from cord blood	blood
23	chr3:52992000-53015800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:52992200-53005600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:52993800-53016800	Weak transcription	Primary B cells from cord blood	blood
26	chr3:52995200-53007000	Weak transcription	Right Ventricle	heart
27	chr3:52997200-53008200	Weak transcription	A549	lung
28	chr3:52999000-53008200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:53001400-53008000	Weak transcription	Osteobl	bone
30	chr3:53001800-53008800	Weak transcription	Brain Substantia Nigra	brain
31	chr3:53002000-53017600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:53002200-53005000	Weak transcription	Brain Angular Gyrus	brain
33	chr3:53002400-53005400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:53002400-53007800	Weak transcription	Hela-S3	cervix
35	chr3:53002400-53012000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:53002400-53013400	Weak transcription	Liver	Liver
37	chr3:53002600-53004800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:53003200-53004800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:53003400-53005400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:53003400-53016000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:53003400-53017000	Weak transcription	Dnd41	blood
42	chr3:53003600-53005200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:53003600-53006000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:53004000-53005800	Weak transcription	Fetal Intestine Large	intestine
45	chr3:53004000-53007800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:53004000-53012200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:53004200-53014800	Weak transcription	Fetal Intestine Small	intestine

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