Variant report

Variant	rs72799507
Chromosome Location	chr2:55488297-55488298
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55485423..55489469-chr2:55495685..55498488,3	MCF-7	breast:
2	chr2:55481770..55484795-chr2:55484832..55488632,4	K562	blood:

Variant related genes	Relation type
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10200120	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056445	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11357	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12052613	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12988617	0.80[ASN][1000 genomes]
rs17852670	0.80[ASN][1000 genomes]
rs2576711	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2576712	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576719	0.83[ASN][1000 genomes]
rs2576721	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2589080	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2589092	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2589093	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2589094	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2589096	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2589100	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2864819	0.90[ASN][1000 genomes]
rs2864826	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2917779	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920967	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34348115	0.80[ASN][1000 genomes]
rs34511570	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4435493	0.81[ASN][1000 genomes]
rs55997390	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56039135	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56384563	0.85[ASN][1000 genomes]
rs62135146	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6545480	0.94[ASN][1000 genomes]
rs6706815	0.81[ASN][1000 genomes]
rs6755515	0.85[ASN][1000 genomes]
rs7597293	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3502708	chr2:55481350-55506212	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3502709	chr2:55481350-55506212	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv525025	chr2:55483020-55505456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs72799507	CLHC1	cis	Adipose Subcutaneous	GTEx
rs72799507	CLHC1	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
3	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
5	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr2:55462200-55490200	Weak transcription	Small Intestine	intestine
7	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:55463800-55490400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:55463800-55494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:55463800-55495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:55464600-55495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:55465400-55490600	Weak transcription	Brain Germinal Matrix	brain
13	chr2:55465600-55494400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:55466000-55493200	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr2:55468200-55493400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:55468400-55493200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:55468400-55494400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:55468600-55494400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:55468800-55493600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:55468800-55494400	Strong transcription	Adipose Nuclei	Adipose
21	chr2:55468800-55494400	Strong transcription	Liver	Liver
22	chr2:55469400-55492600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr2:55470800-55494200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:55472000-55495200	Weak transcription	Psoas Muscle	Psoas
25	chr2:55473600-55490200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:55475400-55490000	Weak transcription	Gastric	stomach
27	chr2:55476000-55495400	Weak transcription	HUVEC	blood vessel
28	chr2:55476600-55490000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:55476600-55495400	Weak transcription	Aorta	Aorta
30	chr2:55476600-55495400	Weak transcription	Fetal Heart	heart
31	chr2:55476600-55495600	Weak transcription	Esophagus	oesophagus
32	chr2:55476800-55490200	Weak transcription	Spleen	Spleen
33	chr2:55476800-55495400	Weak transcription	Fetal Kidney	kidney
34	chr2:55477000-55490200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:55478400-55493400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:55478400-55494800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:55478800-55489200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:55478800-55494200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:55479000-55493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:55480000-55495400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:55480200-55489200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:55480200-55490600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:55480400-55489200	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:55480400-55490000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:55480400-55490200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:55480400-55495600	Weak transcription	Brain Substantia Nigra	brain
47	chr2:55480600-55490200	Weak transcription	NHLF	lung
48	chr2:55481400-55489400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr2:55481400-55490400	Weak transcription	K562	blood
50	chr2:55481400-55490600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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