Variant report

Variant	rs2280680
Chromosome Location	chr7:129549168-129549169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:129548130..129550010-chr7:129589181..129591944,2	MCF-7	breast:
2	chr7:129542833..129545187-chr7:129548253..129550417,2	MCF-7	breast:
3	chr7:129539098..129541114-chr7:129547726..129549879,2	MCF-7	breast:
4	chr7:129548143..129549663-chr7:129591057..129593105,2	MCF-7	breast:
5	chr7:129547818..129550816-chr7:129688251..129690388,2	K562	blood:
6	chr7:129547874..129549625-chr7:129552629..129554432,2	K562	blood:
7	chr7:129544543..129549195-chr7:129554830..129557453,4	K562	blood:

Variant related genes	Relation type
ENSG00000244036	Chromatin interaction
ENSG00000186591	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs16873739	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3807118	0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3807119	0.82[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3817530	0.82[CHB][hapmap];0.83[GIH][hapmap]
rs4728179	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4731633	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4731634	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4731636	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62491490	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62491495	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62491500	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62491519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62491520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62491531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62491534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62491535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62491538	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62491540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62491541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533849	chr7:129462947-129616625	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv831129	chr7:129525406-129702477	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129516200-129584400	Weak transcription	Fetal Brain Male	brain
2	chr7:129518200-129557200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:129518200-129564600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr7:129520800-129551200	Weak transcription	Placenta	Placenta
5	chr7:129529800-129553400	Weak transcription	Brain Germinal Matrix	brain
6	chr7:129530000-129587600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:129537000-129554800	Weak transcription	NHDF-Ad	bronchial
8	chr7:129537200-129552000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:129539600-129554800	Weak transcription	Dnd41	blood
10	chr7:129541000-129552400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:129541400-129551800	Weak transcription	NHLF	lung
12	chr7:129541800-129559200	Weak transcription	Esophagus	oesophagus
13	chr7:129543000-129549200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:129543000-129553600	Weak transcription	Gastric	stomach
15	chr7:129544400-129549200	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr7:129544600-129551200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:129544800-129559400	Weak transcription	Lung	lung
18	chr7:129545400-129553600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:129545800-129550600	Weak transcription	Thymus	Thymus
20	chr7:129545800-129551400	Weak transcription	NHEK	skin
21	chr7:129545800-129553200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr7:129546200-129549200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr7:129546400-129549200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:129546400-129549400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:129546400-129549400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:129546400-129549400	Enhancers	Fetal Heart	heart
27	chr7:129546600-129549400	Enhancers	NH-A	brain
28	chr7:129546600-129549600	Enhancers	Psoas Muscle	Psoas
29	chr7:129546600-129550600	Weak transcription	Fetal Intestine Large	intestine
30	chr7:129546800-129549200	Weak transcription	Fetal Thymus	thymus
31	chr7:129546800-129549400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr7:129547000-129549200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr7:129547000-129549200	Enhancers	Brain Substantia Nigra	brain
34	chr7:129547000-129549400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr7:129547000-129549400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr7:129547000-129549800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr7:129547000-129552400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr7:129547000-129557200	Weak transcription	Colonic Mucosa	Colon
39	chr7:129547000-129563600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr7:129547200-129549200	Weak transcription	Fetal Intestine Small	intestine
41	chr7:129547200-129549600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:129547200-129549600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr7:129547200-129549800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr7:129547200-129549800	Enhancers	K562	blood
45	chr7:129547200-129550800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr7:129547200-129554200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr7:129547400-129549200	Weak transcription	Fetal Muscle Leg	muscle
48	chr7:129547400-129549200	Weak transcription	Ovary	ovary
49	chr7:129547400-129549400	Weak transcription	Stomach Mucosa	stomach
50	chr7:129547400-129549800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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