Variant report

Variant	rs61607068
Chromosome Location	chr3:156542136-156542137
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:156541940-156545935	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156268894..156273100-chr3:156541711..156545313,4	MCF-7	breast:
2	chr3:156527592..156531932-chr3:156540848..156546879,8	MCF-7	breast:

Variant related genes	Relation type
LEKR1	TF binding region
ENSG00000230457	Chromatin interaction
ENSG00000114850	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs13317783	0.83[AFR][1000 genomes]
rs13323819	1.00[AMR][1000 genomes]
rs1397191	1.00[AMR][1000 genomes]
rs16826731	1.00[AMR][1000 genomes]
rs1991618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28695987	1.00[AMR][1000 genomes]
rs56234943	1.00[AMR][1000 genomes]
rs57472927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59077786	0.81[AFR][1000 genomes]
rs60659904	1.00[AMR][1000 genomes]
rs6763560	0.83[AFR][1000 genomes]
rs6763606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6779040	1.00[AMR][1000 genomes]
rs6797924	1.00[AMR][1000 genomes]
rs73873709	1.00[AMR][1000 genomes]
rs73873711	1.00[AMR][1000 genomes]
rs7609776	1.00[AMR][1000 genomes]
rs7610539	1.00[AMR][1000 genomes]
rs7610749	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7620352	1.00[AMR][1000 genomes]
rs7620432	1.00[AMR][1000 genomes]
rs7625660	0.83[AFR][1000 genomes]
rs9811311	0.83[AFR][1000 genomes]
rs9814160	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9818849	0.83[AFR][1000 genomes]
rs9825950	0.86[AFR][1000 genomes]
rs9829961	1.00[AMR][1000 genomes]
rs9834930	1.00[AMR][1000 genomes]
rs9835232	1.00[AMR][1000 genomes]
rs9837209	1.00[AMR][1000 genomes]
rs9841118	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9853712	1.00[AMR][1000 genomes]
rs9855517	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9866769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9870674	1.00[AMR][1000 genomes]
rs9873467	1.00[AMR][1000 genomes]
rs9873640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9876941	0.83[AFR][1000 genomes]
rs9883215	0.86[AFR][1000 genomes]
rs9883478	1.00[AMR][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

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156535400-156543400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:156536200-156543200	Weak transcription	Fetal Kidney	kidney
3	chr3:156536400-156542400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:156536400-156542400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:156536400-156543000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:156536400-156543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:156536400-156543200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:156536400-156543200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:156536400-156543200	Weak transcription	Thymus	Thymus
10	chr3:156537000-156543200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:156537000-156543400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:156537000-156543400	Weak transcription	Liver	Liver
13	chr3:156537000-156543600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:156537000-156543600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:156537200-156542600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:156537600-156542400	Weak transcription	K562	blood
17	chr3:156538000-156543400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:156538600-156543200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:156538600-156543400	Weak transcription	NHLF	lung
20	chr3:156538800-156542200	Weak transcription	A549	lung
21	chr3:156538800-156543200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:156538800-156543200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:156538800-156543200	Weak transcription	NHDF-Ad	bronchial
24	chr3:156538800-156543400	Weak transcription	HSMMtube	muscle
25	chr3:156539000-156542400	Weak transcription	Hela-S3	cervix
26	chr3:156539000-156543200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:156539000-156543200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:156539000-156543200	Weak transcription	HMEC	breast
29	chr3:156539000-156543200	Weak transcription	HSMM	muscle
30	chr3:156539000-156543200	Weak transcription	HUVEC	blood vessel
31	chr3:156539000-156543200	Weak transcription	Osteobl	bone
32	chr3:156539000-156543400	Weak transcription	NH-A	brain
33	chr3:156539200-156543200	Weak transcription	GM12878-XiMat	blood
34	chr3:156539200-156543400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:156540800-156542200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:156541400-156542200	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr3:156541400-156542200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:156541600-156543000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr3:156541800-156542400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:156541800-156542400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:156541800-156543200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:156541800-156543400	Enhancers	Fetal Intestine Large	intestine
43	chr3:156541800-156543600	Enhancers	Fetal Intestine Small	intestine
44	chr3:156541800-156543800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:156542000-156542800	Enhancers	Stomach Mucosa	stomach
46	chr3:156542000-156543400	Enhancers	NHEK	skin

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