Variant report

Variant	rs6727604
Chromosome Location	chr2:99112060-99112061
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	chr2:99099626..99101575-chr2:99110514..99112493,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11885661	1.00[EUR][1000 genomes]
rs11890366	1.00[EUR][1000 genomes]
rs11891148	1.00[EUR][1000 genomes]
rs11901761	1.00[EUR][1000 genomes]
rs13395005	1.00[EUR][1000 genomes]
rs17020532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17030716	1.00[EUR][1000 genomes]
rs17033137	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17034163	1.00[EUR][1000 genomes]
rs17034202	1.00[EUR][1000 genomes]
rs17034261	1.00[EUR][1000 genomes]
rs1847551	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2271041	1.00[EUR][1000 genomes]
rs2871214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35028575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710669	1.00[EUR][1000 genomes]
rs6716095	1.00[EUR][1000 genomes]
rs6730113	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6730953	1.00[EUR][1000 genomes]
rs6739018	1.00[EUR][1000 genomes]
rs6749575	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6749743	1.00[EUR][1000 genomes]
rs6754711	1.00[EUR][1000 genomes]
rs6756034	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6756693	1.00[EUR][1000 genomes]
rs7561785	1.00[EUR][1000 genomes]
rs7570509	1.00[EUR][1000 genomes]
rs7585045	1.00[EUR][1000 genomes]
rs7605114	1.00[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	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1006328	chr2:98977192-99210376	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007244	chr2:99063753-99136472	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99072600-99119600	Weak transcription	Aorta	Aorta
2	chr2:99096800-99113600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:99098400-99115200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:99100400-99121600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:99101000-99115200	Weak transcription	Fetal Lung	lung
6	chr2:99101600-99121200	Weak transcription	Gastric	stomach
7	chr2:99101600-99131400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:99102200-99122200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:99103200-99113200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:99103400-99115200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:99103600-99113400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:99103600-99118400	Weak transcription	HSMMtube	muscle
13	chr2:99104000-99118400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:99105200-99120400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:99106000-99115200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:99106800-99119600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:99106800-99119800	Weak transcription	Pancreas	Pancrea
18	chr2:99107000-99115000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:99108000-99113200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:99108000-99115200	Weak transcription	Small Intestine	intestine
21	chr2:99108000-99120200	Weak transcription	Esophagus	oesophagus
22	chr2:99108200-99118400	Weak transcription	Brain Angular Gyrus	brain
23	chr2:99109200-99113200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:99109400-99112800	Strong transcription	Primary T cells from cord blood	blood
25	chr2:99109400-99115000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:99109400-99115800	ZNF genes & repeats	GM12878-XiMat	blood
27	chr2:99109600-99113200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:99109600-99116800	Weak transcription	Lung	lung
29	chr2:99109800-99113200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:99109800-99113400	Weak transcription	Fetal Stomach	stomach
31	chr2:99109800-99115200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:99110000-99113000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr2:99110400-99112200	Enhancers	Psoas Muscle	Psoas
34	chr2:99110400-99114200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
35	chr2:99110600-99112400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:99110600-99114200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
37	chr2:99110800-99113400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:99111000-99112200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr2:99111000-99112400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:99111000-99112400	Enhancers	Colon Smooth Muscle	Colon
41	chr2:99111000-99112600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:99111000-99113200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:99111000-99113200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:99111000-99113200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:99111000-99113200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:99111000-99113400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr2:99111000-99114800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr2:99111000-99118800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:99111200-99113200	Weak transcription	Fetal Thymus	thymus
50	chr2:99111400-99113600	Weak transcription	Primary T cells fromperipheralblood	blood

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