Variant report

Variant	rs6716749
Chromosome Location	chr2:113389476-113389477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113383343..113387238-chr2:113388797..113391596,3	MCF-7	breast:
2	chr2:113389446..113391358-chr2:113401501..113403528,2	MCF-7	breast:
3	chr2:113347066..113349613-chr2:113387380..113389746,2	K562	blood:
4	chr2:113385104..113391547-chr2:113463938..113470179,6	K562	blood:
5	chr2:113388586..113390776-chr2:113395916..113398828,2	MCF-7	breast:
6	chr2:113388214..113390218-chr2:113391409..113393753,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237753	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000228251	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12987250	0.87[EUR][1000 genomes]
rs13025131	0.91[CEU][hapmap];0.95[GIH][hapmap];0.86[EUR][1000 genomes]
rs13030884	0.97[EUR][1000 genomes]
rs17586834	0.86[EUR][1000 genomes]
rs17587043	0.91[CEU][hapmap];0.95[GIH][hapmap];0.87[EUR][1000 genomes]
rs17587297	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17647292	0.85[EUR][1000 genomes]
rs17647908	0.82[CEU][hapmap]
rs34015418	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35670704	0.88[EUR][1000 genomes]
rs35995321	0.89[EUR][1000 genomes]
rs36079920	0.89[EUR][1000 genomes]
rs36082214	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4405766	0.98[EUR][1000 genomes]
rs58770636	0.91[EUR][1000 genomes]
rs6716762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6737981	0.86[EUR][1000 genomes]
rs71414685	0.86[EUR][1000 genomes]
rs7566777	0.86[EUR][1000 genomes]
rs7607685	0.85[EUR][1000 genomes]
rs7607817	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6716749	AC079922.3	cis	Artery Tibial	GTEx
rs6716749	AC079922.3	cis	Muscle Skeletal	GTEx
rs6716749	AC079922.3	cis	Esophagus Muscularis	GTEx
rs6716749	AC079922.3	cis	lung	GTEx
rs6716749	AC079922.3	cis	Whole Blood	GTEx
rs6716749	AC079922.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113381600-113389600	Enhancers	Placenta	Placenta
2	chr2:113384200-113392400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:113384600-113389800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:113384600-113390000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:113385000-113389600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:113385000-113389800	Enhancers	NHDF-Ad	bronchial
7	chr2:113385000-113396000	Weak transcription	Colonic Mucosa	Colon
8	chr2:113385000-113402600	Weak transcription	Esophagus	oesophagus
9	chr2:113385200-113390600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:113385800-113401800	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:113386600-113390000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:113387400-113389600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:113387400-113389600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:113387400-113389600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr2:113387400-113389800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:113387400-113389800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:113387400-113389800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:113387400-113389800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:113387400-113389800	Enhancers	HSMMtube	muscle
20	chr2:113387600-113389600	Enhancers	H9 Cell Line	embryonic stem cell
21	chr2:113387600-113389600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr2:113387600-113389600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr2:113387600-113389600	Enhancers	Fetal Muscle Leg	muscle
24	chr2:113387600-113389800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr2:113387600-113389800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr2:113387600-113389800	Enhancers	NHLF	lung
27	chr2:113387600-113390000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:113387800-113389600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr2:113387800-113389600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:113387800-113389600	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr2:113387800-113389600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr2:113387800-113389600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr2:113387800-113389800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr2:113387800-113389800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr2:113387800-113389800	Flanking Active TSS	Dnd41	blood
36	chr2:113388000-113389600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:113388000-113389600	Enhancers	Primary B cells from cord blood	blood
38	chr2:113388000-113389600	Enhancers	Fetal Lung	lung
39	chr2:113388000-113389600	Enhancers	Left Ventricle	heart
40	chr2:113388000-113389800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:113388000-113389800	Enhancers	Primary B cells from peripheral blood	blood
42	chr2:113388000-113389800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:113388000-113389800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr2:113388000-113389800	Enhancers	Duodenum Mucosa	Duodenum
45	chr2:113388000-113389800	Enhancers	Fetal Intestine Large	intestine
46	chr2:113388200-113389600	Enhancers	Fetal Kidney	kidney
47	chr2:113388200-113389600	Flanking Active TSS	Osteobl	bone
48	chr2:113388200-113389800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr2:113388400-113389800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr2:113388400-113389800	Flanking Active TSS	GM12878-XiMat	blood

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