Variant report

Variant	rs17037002
Chromosome Location	chr2:48077705-48077706
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48070745..48074263-chr2:48075364..48078166,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MSH6-3	chr2:48077476-48077816	NONHSAT070603

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10495947	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17036996	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17037018	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17037038	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17037055	0.86[YRI][hapmap]
rs17037064	0.86[YRI][hapmap]
rs2134056	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60154625	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60866242	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6704872	1.00[CEU][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6714441	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6723441	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73929251	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7572674	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7587289	0.93[CEU][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv930955	chr2:48040218-48121218	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv523013	chr2:48073117-48146122	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48043400-48088600	Weak transcription	Pancreas	Pancrea
2	chr2:48048600-48080600	Weak transcription	NHLF	lung
3	chr2:48049200-48096000	Weak transcription	Gastric	stomach
4	chr2:48060200-48093000	Weak transcription	Psoas Muscle	Psoas
5	chr2:48061400-48093800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:48062600-48080800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:48063800-48081800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:48063800-48083600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:48064000-48095200	Weak transcription	Spleen	Spleen
10	chr2:48064200-48081800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:48064400-48084800	Weak transcription	NHEK	skin
12	chr2:48065000-48081000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:48065200-48086600	Weak transcription	Fetal Brain Female	brain
14	chr2:48065400-48098200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:48065400-48114000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:48066000-48085200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:48066000-48097400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:48066000-48100400	Weak transcription	Thymus	Thymus
19	chr2:48066200-48080000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:48066200-48080800	Weak transcription	HSMMtube	muscle
21	chr2:48066200-48084000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:48066200-48085400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:48066200-48094600	Weak transcription	Fetal Kidney	kidney
24	chr2:48066400-48083200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:48066400-48085400	Weak transcription	Osteobl	bone
26	chr2:48066400-48088400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:48066400-48092200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:48066400-48097600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:48066800-48080800	Weak transcription	Fetal Lung	lung
30	chr2:48066800-48081000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:48066800-48081400	Weak transcription	NHDF-Ad	bronchial
32	chr2:48066800-48083400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:48066800-48083600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:48066800-48084200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:48066800-48088400	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:48066800-48094200	Weak transcription	HSMM	muscle
37	chr2:48066800-48094400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:48067000-48079000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:48067000-48080600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:48067000-48080600	Weak transcription	A549	lung
41	chr2:48067000-48080800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:48067000-48081200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:48067000-48082400	Weak transcription	NH-A	brain
44	chr2:48067000-48082600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:48067000-48083200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:48067000-48084600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:48067000-48091800	Weak transcription	HUVEC	blood vessel
48	chr2:48067000-48094200	Weak transcription	HMEC	breast
49	chr2:48067000-48094800	Weak transcription	K562	blood
50	chr2:48067000-48095800	Weak transcription	Fetal Thymus	thymus

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