Variant report

Variant	rs344076
Chromosome Location	chr3:156552785-156552786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156552175..156554345-chr3:156554997..156556879,2	MCF-7	breast:
2	chr3:156543994..156545852-chr3:156551932..156553625,2	MCF-7	breast:
3	chr3:156542736..156546133-chr3:156552439..156555764,4	K562	blood:
4	chr3:156541425..156545674-chr3:156551760..156556464,6	K562	blood:

Variant related genes	Relation type
ENSG00000197980	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10212230	0.81[YRI][hapmap]
rs10936040	0.85[YRI][hapmap]
rs11710516	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11717138	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11927500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12634915	0.81[YRI][hapmap]
rs13088978	0.81[YRI][hapmap]
rs13321802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13322318	0.81[YRI][hapmap]
rs1355280	1.00[CHB][hapmap]
rs1430412	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1510270	1.00[CHB][hapmap]
rs168248	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16826858	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16826864	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16826899	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];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16826906	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16826948	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs171077	0.83[ASN][1000 genomes]
rs171080	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs180746	0.83[ASN][1000 genomes]
rs180747	1.00[CHB][hapmap]
rs182936	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs184677	1.00[CHB][hapmap]
rs193198	1.00[CHB][hapmap]
rs193423	1.00[CHB][hapmap]
rs2054881	1.00[CHB][hapmap]
rs2129909	1.00[CHB][hapmap]
rs2321290	0.85[YRI][hapmap]
rs237246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2633815	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2653817	0.87[GIH][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.81[AFR][1000 genomes]
rs2665390	1.00[CHB][hapmap]
rs28661978	1.00[ASN][1000 genomes]
rs2874490	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2874491	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs343992	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs344005	1.00[CHB][hapmap]
rs344006	1.00[CHB][hapmap]
rs344008	1.00[CHB][hapmap]
rs344009	1.00[CHB][hapmap]
rs344010	1.00[CHB][hapmap]
rs344011	1.00[CHB][hapmap]
rs344012	1.00[CHB][hapmap]
rs344013	1.00[CHB][hapmap]
rs344014	1.00[CHB][hapmap]
rs344015	1.00[CHB][hapmap]
rs344016	1.00[CHB][hapmap]
rs344017	1.00[CHB][hapmap]
rs344023	0.83[ASN][1000 genomes]
rs344047	0.83[ASN][1000 genomes]
rs344048	0.83[ASN][1000 genomes]
rs344049	0.83[ASN][1000 genomes]
rs344050	0.83[ASN][1000 genomes]
rs344052	1.00[CHB][hapmap]
rs344053	1.00[CHB][hapmap]
rs344054	1.00[CHB][hapmap]
rs344055	1.00[CHB][hapmap]
rs344058	1.00[CHB][hapmap]
rs344059	1.00[CHB][hapmap]
rs344060	1.00[CHB][hapmap]
rs344061	1.00[CHB][hapmap]
rs344062	1.00[CHB][hapmap]
rs344063	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs344064	1.00[CHB][hapmap]
rs344065	1.00[CHB][hapmap]
rs344066	1.00[CHB][hapmap]
rs344068	1.00[CHB][hapmap]
rs344069	1.00[CHB][hapmap]
rs344070	1.00[CHB][hapmap]
rs344071	0.94[CEU][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344072	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs344074	1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs344077	1.00[ASN][1000 genomes]
rs344078	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs344081	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs344083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344085	0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs344086	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs344088	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs344089	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs344090	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs344091	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs344092	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs344093	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3796172	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs414683	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs419287	1.00[CHB][hapmap]
rs427384	1.00[CHB][hapmap]
rs4429586	1.00[CHB][hapmap]
rs4441614	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4680298	0.83[CHD][hapmap]
rs4680299	0.83[CHD][hapmap]
rs4680304	0.84[ASN][1000 genomes]
rs491423	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];0.99[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55850252	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58207863	0.84[ASN][1000 genomes]
rs59244547	1.00[ASN][1000 genomes]
rs6441092	0.83[CHD][hapmap]
rs6441095	1.00[CHB][hapmap]
rs6441099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441100	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.99[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6441103	0.97[GIH][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6441104	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6763233	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6763644	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];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6774702	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6786167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6787535	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6787952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6792917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6795327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6795516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6799457	0.83[CHD][hapmap]
rs6802042	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6802511	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7426821	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7609851	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7616633	0.81[GIH][hapmap]
rs7618306	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7621699	0.89[ASN][1000 genomes]
rs7630909	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7635521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7640994	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7650127	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.84[TSI][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs978108	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs9810194	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9823112	1.00[CHB][hapmap]
rs9841269	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9844054	0.81[YRI][hapmap]
rs9847187	0.81[YRI][hapmap]
rs9847692	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9861359	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9871817	0.81[YRI][hapmap]
rs9876010	0.80[YRI][hapmap]
rs9878585	0.81[YRI][hapmap]
rs9878709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs344076	LEKR1	cis	Heart Left Ventricle	GTEx
rs344076	VEPH1	cis	cerebellum	SCAN
rs344076	LEKR1	cis	cerebellum	SCAN
rs344076	LEKR1	cis	parietal	SCAN
rs344076	LEKR1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156545000-156559600	Weak transcription	Pancreas	Pancrea
2	chr3:156545600-156554000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:156545800-156558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:156550800-156553000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:156552000-156553200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
6	chr3:156552000-156555400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:156552200-156554000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:156552400-156553600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr3:156552400-156553600	Enhancers	GM12878-XiMat	blood
10	chr3:156552400-156554200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
11	chr3:156552600-156553200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
12	chr3:156552600-156554200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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