Variant report

Variant	rs61782405
Chromosome Location	chr1:94285286-94285287
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	chr1:94095273..94097251-chr1:94284521..94286111,2	MCF-7	breast:
2	chr1:94285157..94287017-chr1:94328663..94330459,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10489605	0.83[ASN][1000 genomes]
rs10874795	0.97[ASN][1000 genomes]
rs1108527	0.83[EUR][1000 genomes]
rs1108528	0.84[EUR][1000 genomes]
rs11164994	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165001	0.91[ASN][1000 genomes]
rs11165019	0.97[ASN][1000 genomes]
rs12079584	0.97[ASN][1000 genomes]
rs12239830	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17100397	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110408	0.91[ASN][1000 genomes]
rs17304770	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17878271	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17878294	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17881810	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17884788	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17885151	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17886352	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1877605	0.86[EUR][1000 genomes]
rs2223908	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761913	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41292665	0.92[EUR][1000 genomes]
rs4615846	0.82[ASN][1000 genomes]
rs57870303	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61425457	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61781048	0.83[EUR][1000 genomes]
rs61781049	0.96[EUR][1000 genomes]
rs61781051	0.98[EUR][1000 genomes]
rs61781053	1.00[EUR][1000 genomes]
rs61781054	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61781055	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61781056	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61781057	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782162	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782163	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782164	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782165	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782398	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782399	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782400	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782403	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782404	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782410	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782413	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782449	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61782450	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782451	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782458	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782459	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6660794	0.91[ASN][1000 genomes]
rs6671839	0.91[ASN][1000 genomes]
rs6674149	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6689215	0.89[ASN][1000 genomes]
rs6689746	0.91[ASN][1000 genomes]
rs6703468	0.91[ASN][1000 genomes]
rs717913	0.91[ASN][1000 genomes]
rs72723114	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723118	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723125	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723138	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723165	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723169	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723178	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72967397	0.97[ASN][1000 genomes]
rs7523682	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546822	chr1:94246577-94289863	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1815663	chr1:94246577-94291252	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1877	chr1:94247756-94292908	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv508415	chr1:94256122-94305339	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1802380	chr1:94272119-94291252	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1822452	chr1:94278128-94320233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61782405	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94279600-94302800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:94280000-94285600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:94280000-94290000	Weak transcription	Brain Angular Gyrus	brain
4	chr1:94280800-94285800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:94281200-94289600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:94281400-94285600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:94281400-94285800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:94281600-94285400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:94281800-94285600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:94282400-94285800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:94283000-94285400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:94283000-94285600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:94283000-94286000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:94283000-94288400	Weak transcription	NHDF-Ad	bronchial
15	chr1:94283200-94286000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:94283200-94286600	Weak transcription	A549	lung
17	chr1:94283200-94286800	Weak transcription	HSMMtube	muscle
18	chr1:94283400-94285800	Weak transcription	NH-A	brain
19	chr1:94283400-94286800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:94283400-94290000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:94283400-94310000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:94283600-94286800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:94283600-94286800	Weak transcription	Right Atrium	heart
24	chr1:94283600-94286800	Weak transcription	HSMM	muscle
25	chr1:94283600-94287800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:94283600-94288400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:94283600-94293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:94284000-94285600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:94284000-94285800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:94284000-94294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:94284200-94286000	Weak transcription	HUVEC	blood vessel
32	chr1:94284200-94286400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr1:94284200-94292200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:94284200-94306200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:94284200-94311200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:94284400-94285400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:94284400-94285600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:94284400-94286600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:94284400-94287400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:94284400-94289600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:94284400-94296000	Weak transcription	Fetal Intestine Small	intestine
42	chr1:94284600-94287000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:94285000-94286000	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr1:94285000-94286200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:94285000-94287000	Weak transcription	HMEC	breast
46	chr1:94285000-94287400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:94285000-94288400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:94285200-94285600	Weak transcription	Placenta	Placenta
49	chr1:94285200-94285800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:94285200-94286000	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links