Variant report

Variant	rs60409549
Chromosome Location	chr7:3901949-3901950
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	chr7:3895859..3898107-chr7:3900891..3903068,3	MCF-7	breast:

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10226220	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10230252	1.00[AMR][1000 genomes]
rs10231172	1.00[AMR][1000 genomes]
rs10232161	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10232222	1.00[AMR][1000 genomes]
rs10232460	1.00[AMR][1000 genomes]
rs10232479	1.00[AMR][1000 genomes]
rs10233390	0.91[AFR][1000 genomes]
rs10235415	1.00[AMR][1000 genomes]
rs10236208	1.00[AMR][1000 genomes]
rs10236726	1.00[AMR][1000 genomes]
rs10237072	1.00[AMR][1000 genomes]
rs10237207	1.00[AMR][1000 genomes]
rs10237489	1.00[AMR][1000 genomes]
rs10237769	1.00[AMR][1000 genomes]
rs10238790	1.00[AMR][1000 genomes]
rs10239119	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10239349	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10239755	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10240764	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10240770	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10240776	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10244131	1.00[AMR][1000 genomes]
rs10244910	1.00[AMR][1000 genomes]
rs10246377	1.00[AMR][1000 genomes]
rs10247342	1.00[AMR][1000 genomes]
rs10248032	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10249486	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10249617	1.00[AMR][1000 genomes]
rs10250749	1.00[AMR][1000 genomes]
rs10250969	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10250990	1.00[AMR][1000 genomes]
rs10251860	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10252145	1.00[AMR][1000 genomes]
rs10254515	1.00[AMR][1000 genomes]
rs10254942	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10259149	1.00[AMR][1000 genomes]
rs10259421	1.00[AMR][1000 genomes]
rs10259908	1.00[AMR][1000 genomes]
rs10260208	0.81[AFR][1000 genomes]
rs10260973	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10261101	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10262755	1.00[AMR][1000 genomes]
rs10262756	1.00[AMR][1000 genomes]
rs10264034	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10265265	1.00[AMR][1000 genomes]
rs10266546	1.00[AMR][1000 genomes]
rs10269172	1.00[AMR][1000 genomes]
rs10269554	1.00[AMR][1000 genomes]
rs10269925	1.00[AMR][1000 genomes]
rs10271361	1.00[AMR][1000 genomes]
rs10271525	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10274442	1.00[AMR][1000 genomes]
rs10274450	1.00[AMR][1000 genomes]
rs10275943	1.00[AMR][1000 genomes]
rs10277140	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10277615	1.00[AMR][1000 genomes]
rs10277730	1.00[AMR][1000 genomes]
rs10281035	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10281383	1.00[AMR][1000 genomes]
rs10282240	1.00[AMR][1000 genomes]
rs10282727	1.00[AMR][1000 genomes]
rs10479827	1.00[AMR][1000 genomes]
rs10479828	1.00[AMR][1000 genomes]
rs11505318	1.00[AMR][1000 genomes]
rs11505319	1.00[AMR][1000 genomes]
rs11505320	1.00[AMR][1000 genomes]
rs11505321	1.00[AMR][1000 genomes]
rs11505480	1.00[AMR][1000 genomes]
rs11505481	1.00[AMR][1000 genomes]
rs12333365	1.00[AMR][1000 genomes]
rs12333373	1.00[AMR][1000 genomes]
rs12333491	1.00[AMR][1000 genomes]
rs12333534	1.00[AMR][1000 genomes]
rs12333847	1.00[AMR][1000 genomes]
rs12333850	1.00[AMR][1000 genomes]
rs12333854	1.00[AMR][1000 genomes]
rs16871049	1.00[AMR][1000 genomes]
rs28408018	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28462157	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28491068	1.00[AMR][1000 genomes]
rs28496653	1.00[AMR][1000 genomes]
rs28507850	1.00[AMR][1000 genomes]
rs28532947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28541657	1.00[AMR][1000 genomes]
rs28554772	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28558397	1.00[AMR][1000 genomes]
rs28560779	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28563149	1.00[AMR][1000 genomes]
rs28565971	1.00[AFR][1000 genomes]
rs28568652	1.00[AMR][1000 genomes]
rs28570515	1.00[AMR][1000 genomes]
rs28578945	1.00[AMR][1000 genomes]
rs28581916	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28587155	1.00[AMR][1000 genomes]
rs28593083	1.00[AMR][1000 genomes]
rs28656287	1.00[AMR][1000 genomes]
rs28656426	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28692586	1.00[AMR][1000 genomes]
rs28715920	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28753192	1.00[AMR][1000 genomes]
rs28765162	1.00[AMR][1000 genomes]
rs28833830	1.00[AMR][1000 genomes]
rs28839918	1.00[AMR][1000 genomes]
rs28846162	1.00[AMR][1000 genomes]
rs28856279	1.00[AMR][1000 genomes]
rs28884793	1.00[AMR][1000 genomes]
rs34758548	1.00[AMR][1000 genomes]
rs56740561	1.00[AMR][1000 genomes]
rs57744825	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58738480	1.00[AMR][1000 genomes]
rs59292244	1.00[AMR][1000 genomes]
rs59408720	1.00[AMR][1000 genomes]
rs60243310	1.00[AMR][1000 genomes]
rs9655002	1.00[AMR][1000 genomes]
rs9655328	1.00[AMR][1000 genomes]
rs9655329	1.00[AMR][1000 genomes]
rs9655341	1.00[AMR][1000 genomes]
rs9655342	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1027624	chr7:3808366-3923408	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv538684	chr7:3808366-3923408	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv887336	chr7:3870810-3934909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv887337	chr7:3886254-3934909	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1019190	chr7:3896634-3943566	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3900200-3902600	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr7:3900600-3902000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:3900600-3902200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:3900600-3902200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr7:3900600-3902400	Enhancers	Colon Smooth Muscle	Colon
6	chr7:3900600-3902800	Enhancers	H9 Cell Line	embryonic stem cell
7	chr7:3900600-3902800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr7:3900800-3902200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:3901000-3902000	Enhancers	Fetal Stomach	stomach
10	chr7:3901000-3902400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr7:3901000-3902400	Enhancers	Adipose Nuclei	Adipose
12	chr7:3901000-3902600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr7:3901000-3902800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr7:3901000-3902800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr7:3901200-3902200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:3901200-3902200	Enhancers	NHEK	skin
17	chr7:3901200-3902400	Weak transcription	Lung	lung
18	chr7:3901200-3902600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:3901200-3902600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr7:3901200-3902800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr7:3901200-3902800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr7:3901200-3959600	Weak transcription	Pancreas	Pancrea
23	chr7:3901400-3902000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:3901400-3902000	Enhancers	Brain Anterior Caudate	brain
25	chr7:3901400-3902000	Enhancers	Right Atrium	heart
26	chr7:3901400-3902000	Active TSS	Stomach Smooth Muscle	stomach
27	chr7:3901400-3902200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr7:3901400-3902200	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr7:3901400-3902200	Enhancers	Fetal Kidney	kidney
30	chr7:3901600-3902000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:3901600-3902000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:3901600-3902000	Enhancers	Aorta	Aorta
33	chr7:3901600-3902200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:3901600-3902200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:3901600-3902200	Flanking Active TSS	Fetal Lung	lung
36	chr7:3901600-3902200	Enhancers	Fetal Muscle Leg	muscle
37	chr7:3901800-3902000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:3901800-3902200	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links