Variant report

Variant	rs344074
Chromosome Location	chr3:156548657-156548658
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156537180..156540050-chr3:156547950..156549740,2	K562	blood:
2	chr3:156544049..156546693-chr3:156547441..156549158,2	K562	blood:
3	chr3:156532457..156535368-chr3:156548471..156550364,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240875	Chromatin interaction
ENSG00000197980	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs11710516	1.00[CHB][hapmap]
rs11927500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13321802	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs1355280	1.00[CHB][hapmap]
rs1430410	0.82[YRI][hapmap]
rs1510270	1.00[CHB][hapmap]
rs168248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16826858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16826864	1.00[CHB][hapmap]
rs16826899	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs16826906	1.00[CHB][hapmap]
rs16826948	1.00[CHB][hapmap]
rs171080	1.00[CHB][hapmap]
rs180747	1.00[CHB][hapmap]
rs182936	1.00[CHB][hapmap]
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]
rs2321395	0.89[ASN][1000 genomes]
rs237246	1.00[CHB][hapmap]
rs2633815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2653817	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]
rs2665390	1.00[CHB][hapmap]
rs2874490	1.00[CHB][hapmap]
rs2874491	1.00[CHB][hapmap]
rs343992	1.00[CHB][hapmap]
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]
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]
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	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs344072	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs344076	1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs344078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs344081	1.00[CHB][hapmap]
rs344083	1.00[CHB][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs344086	1.00[CHB][hapmap]
rs344089	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs344090	1.00[CHB][hapmap]
rs344091	1.00[CHB][hapmap]
rs344092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs414683	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs419287	1.00[CHB][hapmap]
rs427384	1.00[CHB][hapmap]
rs4429586	1.00[CHB][hapmap]
rs4441614	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs491423	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs58207863	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6441095	1.00[CHB][hapmap]
rs6441099	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs6441100	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6441103	0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs6441104	1.00[CHB][hapmap]
rs6763233	1.00[CHB][hapmap]
rs6763644	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs6776157	0.80[YRI][hapmap]
rs6786167	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs6787535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6787952	1.00[CHB][hapmap]
rs6792917	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs6795327	1.00[CHB][hapmap]
rs6795516	1.00[CHB][hapmap]
rs6802511	1.00[CHB][hapmap]
rs7426821	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7609851	1.00[CHB][hapmap]
rs7630909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7635521	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs7640994	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7641929	0.80[YRI][hapmap]
rs7650127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs978108	1.00[CHB][hapmap]
rs9810194	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9820830	0.81[YRI][hapmap]
rs9823112	1.00[CHB][hapmap]
rs9858861	0.82[YRI][hapmap]
rs9861359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9874866	0.81[YRI][hapmap]
rs9878709	1.00[CHB][hapmap];0.81[YRI][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs344074	LEKR1	cis	Heart Left Ventricle	GTEx
rs344074	LINC00886	cis	Artery Aorta	GTEx
rs344074	LINC00886	cis	Artery Tibial	GTEx
rs344074	LEKR1	cis	Thyroid	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156545000-156559600	Weak transcription	Pancreas	Pancrea
2	chr3:156545200-156549800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:156545400-156551000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:156545600-156554000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:156545800-156558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:156546000-156549400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:156546000-156549800	Weak transcription	GM12878-XiMat	blood
8	chr3:156547000-156550200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:156548000-156549000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
10	chr3:156548000-156550200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr3:156548000-156551200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr3:156548400-156548800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr3:156548400-156549000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr3:156548600-156548800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
15	chr3:156548600-156549200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:156548600-156550000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:156548600-156550000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links