Variant report

Variant	rs12664121
Chromosome Location	chr6:12169415-12169416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:12162639..12165269-chr6:12167359..12169995,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12661851	0.89[ASN][1000 genomes]
rs12662314	0.83[AMR][1000 genomes]
rs12663812	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12664849	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16872348	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2157492	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2327512	0.83[AMR][1000 genomes]
rs28769650	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3777756	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3777757	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3777764	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3777767	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3777772	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3777774	0.83[AMR][1000 genomes]
rs3777777	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3800499	0.82[AMR][1000 genomes]
rs4317394	0.82[AMR][1000 genomes]
rs4443504	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4484521	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55637995	0.82[AMR][1000 genomes]
rs60122380	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6917623	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6931770	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72828103	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72828104	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72828110	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7449638	0.84[AMR][1000 genomes]
rs7741589	0.82[AMR][1000 genomes];0.80[ASN][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	nsv830586	chr6:12130076-12295334	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv3409171	chr6:12166991-12169839	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv3343064	chr6:12167191-12169614	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12160800-12170800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:12161400-12175800	Weak transcription	Brain Substantia Nigra	brain
3	chr6:12164000-12170600	Weak transcription	Brain Anterior Caudate	brain
4	chr6:12164000-12173200	Weak transcription	NH-A	brain
5	chr6:12164200-12174200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:12164200-12174800	Weak transcription	HMEC	breast
7	chr6:12164400-12169600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:12164400-12170400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:12164400-12174800	Weak transcription	NHEK	skin
10	chr6:12164600-12170400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:12164600-12170600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:12164600-12170600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:12164600-12170600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:12164600-12170800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:12164600-12170800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:12164600-12170800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:12164600-12171000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:12164600-12171800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:12164600-12172200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:12164600-12172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:12164600-12173800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:12164600-12174000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:12164600-12175800	Weak transcription	HSMMtube	muscle
24	chr6:12164600-12176000	Weak transcription	Gastric	stomach
25	chr6:12164800-12170400	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:12164800-12170600	Weak transcription	Adipose Nuclei	Adipose
27	chr6:12164800-12170800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:12164800-12170800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:12164800-12171000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:12164800-12171200	Weak transcription	Fetal Brain Female	brain
31	chr6:12164800-12171600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:12164800-12171800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:12164800-12173400	Weak transcription	Fetal Kidney	kidney
34	chr6:12164800-12174000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:12164800-12175000	Weak transcription	NHDF-Ad	bronchial
36	chr6:12164800-12175200	Weak transcription	HSMM	muscle
37	chr6:12164800-12179800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:12164800-12180200	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:12164800-12185200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:12165000-12171000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:12165000-12171200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr6:12165000-12171600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:12165200-12170000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:12165400-12170600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:12165400-12170800	Weak transcription	Liver	Liver
46	chr6:12165600-12174800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:12166000-12174800	Weak transcription	A549	lung
48	chr6:12166200-12170800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:12166200-12171000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:12166200-12174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links