Variant report

Variant	rs6893195
Chromosome Location	chr5:127609109-127609110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127609023..127610896-chr5:127612305..127614881,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10038028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10041869	1.00[JPT][hapmap]
rs10044959	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10055617	1.00[JPT][hapmap]
rs10057405	0.91[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10057855	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs10059301	1.00[JPT][hapmap]
rs10062686	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10063393	1.00[JPT][hapmap]
rs10070076	1.00[JPT][hapmap]
rs10074194	1.00[JPT][hapmap]
rs10076728	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10077809	1.00[CHB][hapmap]
rs10477683	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10477684	1.00[JPT][hapmap]
rs10478811	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10519994	1.00[JPT][hapmap]
rs11951790	1.00[JPT][hapmap]
rs11951921	1.00[JPT][hapmap]
rs13305	1.00[CHB][hapmap]
rs1396477	1.00[JPT][hapmap]
rs1561006	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs17164115	1.00[JPT][hapmap]
rs17608692	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs17676426	0.91[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1848501	1.00[JPT][hapmap]
rs1978439	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28579194	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28800517	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs374748	1.00[JPT][hapmap]
rs3792871	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs3792873	1.00[JPT][hapmap]
rs3816905	0.88[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs3909897	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes]
rs6873360	1.00[JPT][hapmap]
rs6883276	1.00[JPT][hapmap]
rs7288	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9327476	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs989548	1.00[JPT][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	nsv830482	chr5:127475398-127665377	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv599697	chr5:127563563-127731210	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv830483	chr5:127595570-127705124	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6893195	FBN2	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127588800-127613400	Weak transcription	Ovary	ovary
2	chr5:127589000-127670200	Weak transcription	NHDF-Ad	bronchial
3	chr5:127589200-127612200	Weak transcription	Osteobl	bone
4	chr5:127592600-127614600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:127592800-127612200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr5:127592800-127624400	Weak transcription	A549	lung
7	chr5:127592800-127631600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:127593000-127613400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:127593800-127635200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:127594800-127613600	Weak transcription	HMEC	breast
11	chr5:127596200-127623800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:127598800-127611600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:127598800-127622600	Weak transcription	Fetal Intestine Large	intestine
14	chr5:127598800-127623800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:127599000-127611600	Weak transcription	NHEK	skin
16	chr5:127599000-127612000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:127599200-127611600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:127599200-127613600	Weak transcription	Fetal Kidney	kidney
19	chr5:127599200-127622400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:127599200-127623000	Weak transcription	Fetal Intestine Small	intestine
21	chr5:127599400-127612200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:127599400-127624200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:127599400-127624200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:127600800-127624200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:127601000-127609200	Weak transcription	Fetal Stomach	stomach
26	chr5:127603600-127610400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:127605200-127614600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr5:127605200-127628800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr5:127605400-127617200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:127606600-127610000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr5:127606800-127610600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:127607000-127616600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:127607200-127611600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:127607200-127611800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:127607200-127616400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:127607400-127609200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:127607600-127610400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:127607800-127612400	Weak transcription	HUVEC	blood vessel
39	chr5:127608000-127610200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:127608000-127611600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:127608000-127612200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr5:127608000-127612200	Weak transcription	Fetal Muscle Leg	muscle
43	chr5:127608000-127613400	Weak transcription	Left Ventricle	heart
44	chr5:127608000-127622200	Weak transcription	Fetal Lung	lung
45	chr5:127608000-127629600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:127608400-127611200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr5:127608600-127616600	Strong transcription	Placenta	Placenta
48	chr5:127608800-127610000	Genic enhancers	Fetal Heart	heart
49	chr5:127608800-127610000	Strong transcription	NH-A	brain
50	chr5:127608800-127610200	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links