Variant report

Variant	rs344071
Chromosome Location	chr3:156544584-156544585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:156542707..156546513-chr3:156875626..156880471,4	K562	blood:
2	chr3:156398881..156401137-chr3:156542792..156545641,2	MCF-7	breast:
3	chr3:156268894..156273100-chr3:156541711..156545313,4	MCF-7	breast:
4	chr3:156392291..156392861-chr3:156543900..156544874,2	MCF-7	breast:
5	chr1:15943186..15944074-chr3:156543911..156544904,2	Hela-S3	cervix:
6	chr3:156543166..156544685-chr3:156806392..156807926,2	K562	blood:
7	chr14:92506095..92507002-chr3:156544066..156544649,2	Hela-S3	cervix:
8	chr3:156390293..156396385-chr3:156542364..156548172,18	MCF-7	breast:
9	chr3:156527949..156530289-chr3:156543460..156546861,3	K562	blood:
10	chr3:156390535..156395368-chr3:156542467..156546251,7	MCF-7	breast:
11	chr3:156527592..156531932-chr3:156540848..156546879,8	MCF-7	breast:
12	chr3:156543622..156545874-chr3:156870977..156873628,2	MCF-7	breast:
13	chr3:156398799..156400378-chr3:156543351..156545988,2	MCF-7	breast:
14	chr3:156542698..156545519-chr3:156890354..156893395,4	K562	blood:
15	chr3:156391537..156393857-chr3:156543728..156545632,2	K562	blood:
16	chr3:156391796..156394617-chr3:156542307..156544876,4	K562	blood:
17	chr22:18121346..18122033-chr3:156543806..156544636,2	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-6F2.7.1-2	chr3:156544471-156544669	NONHSAT092873

No data

Variant related genes	Relation type
ENSG00000197312	Chromatin interaction
ENSG00000230457	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000222675	Chromatin interaction
ENSG00000114850	Chromatin interaction
ENSG00000243176	Chromatin interaction
ENSG00000099968	Chromatin interaction
ENSG00000100815	Chromatin interaction
ENSG00000201778	Chromatin interaction
ENSG00000241135	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13321802	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1430410	0.83[YRI][hapmap]
rs168248	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16826899	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2321395	0.83[ASN][1000 genomes]
rs2653817	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	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs344074	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]
rs344076	0.94[CEU][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344078	0.81[AFR][1000 genomes]
rs344083	0.94[CEU][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs344093	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs491423	0.94[CEU][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55850252	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6441099	0.94[CEU][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6763644	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6774702	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6776157	0.81[YRI][hapmap]
rs6786167	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6792917	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7635521	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7641929	0.81[YRI][hapmap]
rs9820830	0.81[YRI][hapmap]
rs9841269	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9858861	0.83[YRI][hapmap]
rs9874866	0.81[YRI][hapmap]
rs9878709	0.94[CEU][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs344071	LEKR1	cis	Heart Left Ventricle	GTEx
rs344071	LEKR1	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156543000-156545400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr3:156543200-156544600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:156543200-156544800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr3:156543200-156545000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:156543200-156545200	Active TSS	Primary T killer memory cells from peripheral blood	blood
6	chr3:156543200-156545200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:156543200-156545200	Flanking Active TSS	HUVEC	blood vessel
8	chr3:156543200-156545400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:156543400-156544600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:156543400-156544600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:156543400-156544600	Active TSS	Brain Germinal Matrix	brain
12	chr3:156543400-156544600	Active TSS	Brain Substantia Nigra	brain
13	chr3:156543400-156544600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr3:156543400-156544800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr3:156543400-156544800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr3:156543400-156544800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:156543400-156544800	Active TSS	Colon Smooth Muscle	Colon
18	chr3:156543400-156545000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr3:156543400-156545000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:156543400-156545000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:156543400-156545000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr3:156543400-156545000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:156543400-156545000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:156543400-156545000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:156543400-156545000	Active TSS	Colonic Mucosa	Colon
26	chr3:156543400-156545000	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:156543400-156545000	Active TSS	Rectal Smooth Muscle	rectum
28	chr3:156543400-156545000	Active TSS	Right Atrium	heart
29	chr3:156543400-156545200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr3:156543400-156545200	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:156543400-156545200	Flanking Active TSS	NH-A	brain
32	chr3:156543400-156545200	Flanking Active TSS	NHEK	skin
33	chr3:156543400-156545400	Active TSS	Fetal Brain Male	brain
34	chr3:156543600-156544600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:156543600-156544600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:156543600-156544600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr3:156543600-156544600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:156543600-156544600	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr3:156543600-156544600	Active TSS	Brain Anterior Caudate	brain
40	chr3:156543600-156544600	Active TSS	Duodenum Mucosa	Duodenum
41	chr3:156543600-156544600	Active TSS	Lung	lung
42	chr3:156543600-156544600	Active TSS	HSMMtube	muscle
43	chr3:156543600-156544800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:156543600-156544800	Active TSS	Liver	Liver
45	chr3:156543600-156544800	Active TSS	Brain Hippocampus Middle	brain
46	chr3:156543600-156544800	Active TSS	Esophagus	oesophagus
47	chr3:156543600-156544800	Active TSS	Psoas Muscle	Psoas
48	chr3:156543600-156544800	Active TSS	Small Intestine	intestine
49	chr3:156543600-156545000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
50	chr3:156543600-156545000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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