Variant report

Variant	rs28492942
Chromosome Location	chr7:39999630-39999631
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39999018..40002091-chr7:40005223..40009207,3	K562	blood:
2	chr7:39987907..39993068-chr7:39995715..40000293,13	MCF-7	breast:
3	chr7:39992254..39999333-chr7:39999543..40002599,8	K562	blood:
4	chr7:39994702..39997445-chr7:39998087..39999888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259826	Chromatin interaction
ENSG00000065883	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10046564	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10224206	0.95[EUR][1000 genomes]
rs10225492	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235989	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10239324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247292	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253590	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272514	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277853	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10279016	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082023	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12701787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231977	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13239106	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241453	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310449	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310480	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17434388	0.82[EUR][1000 genomes]
rs17435812	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496226	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496247	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17526699	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140254	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329611	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28547436	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638437	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34326687	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34470312	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748607	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35052806	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35082351	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35226291	0.81[EUR][1000 genomes]
rs35618050	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273753	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4428576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4481477	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947071	0.83[EUR][1000 genomes]
rs73127832	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73127862	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773382	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780996	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794792	0.81[EUR][1000 genomes]
rs7811585	0.81[EUR][1000 genomes]
rs809558	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs878785	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9639817	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9639820	0.97[EUR][1000 genomes]
rs9655407	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9690347	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9986996	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986997	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39991800-40000200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:39991800-40000800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:39991800-40005200	Weak transcription	Lung	lung
4	chr7:39992000-40006400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:39992600-40001200	Weak transcription	Placenta	Placenta
6	chr7:39993400-40000000	Weak transcription	Fetal Thymus	thymus
7	chr7:39993400-40001000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:39993600-39999800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr7:39993600-40000000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr7:39993600-40048200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:39993800-40000000	Weak transcription	HSMMtube	muscle
12	chr7:39993800-40000800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr7:39993800-40000800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:39994000-40000800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:39994200-40008000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:39994200-40027200	Weak transcription	HSMM	muscle
17	chr7:39994400-40000600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:39994600-40000800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr7:39994600-40000800	Weak transcription	Thymus	Thymus
20	chr7:39994600-40009000	Weak transcription	HMEC	breast
21	chr7:39994800-40000800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr7:39994800-40006600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr7:39994800-40008000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:39994800-40008000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:39994800-40008400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:39994800-40008400	Weak transcription	NHEK	skin
27	chr7:39994800-40018000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr7:39995000-40001000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:39995000-40001000	Weak transcription	Brain Germinal Matrix	brain
30	chr7:39995000-40008000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr7:39995000-40009000	Weak transcription	Osteobl	bone
32	chr7:39995000-40018200	Weak transcription	Spleen	Spleen
33	chr7:39995200-39999800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr7:39995200-39999800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:39995200-40000400	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr7:39995200-40000800	Weak transcription	Fetal Muscle Leg	muscle
37	chr7:39995200-40000800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr7:39995200-40000800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr7:39995200-40001000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr7:39995200-40001400	Weak transcription	HUVEC	blood vessel
41	chr7:39995200-40002400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr7:39995200-40009000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:39995200-40010400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr7:39995200-40042600	Weak transcription	K562	blood
45	chr7:39995600-40007800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:39996000-40008800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr7:39996600-40008000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:39996800-40000600	Weak transcription	Ovary	ovary
49	chr7:39996800-40002600	Weak transcription	Fetal Intestine Large	intestine
50	chr7:39996800-40003000	Weak transcription	Fetal Brain Male	brain

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