Variant report

Variant	rs599861
Chromosome Location	chr18:9605176-9605177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9604914..9606998-chr18:9897522..9900316,2	K562	blood:
2	chr18:9603204..9605560-chr18:9708114..9710476,2	K562	blood:
3	chr18:9602295..9606145-chr18:9613242..9615540,3	MCF-7	breast:
4	chr18:9604425..9606972-chr18:9949570..9951578,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RALBP1-4	chr18:9604875-9605333	l_1522_chr18:9604874-9609362_testes

Variant related genes	Relation type
ENSG00000154845	Chromatin interaction
ENSG00000168461	Chromatin interaction
ENSG00000263627	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11081489	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1662885	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1787165	0.81[ASN][1000 genomes]
rs1787166	0.89[ASN][1000 genomes]
rs2028661	1.00[ASN][1000 genomes]
rs2028662	1.00[ASN][1000 genomes]
rs2028663	1.00[ASN][1000 genomes]
rs2289684	1.00[ASN][1000 genomes]
rs2903504	0.84[EUR][1000 genomes]
rs328995	0.83[AFR][1000 genomes]
rs329002	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329004	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329008	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs329023	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs329024	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329033	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35444634	1.00[ASN][1000 genomes]
rs407530	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs428598	1.00[ASN][1000 genomes]
rs583306	1.00[ASN][1000 genomes]
rs586544	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs589559	0.89[ASN][1000 genomes]
rs610564	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62088919	0.80[AMR][1000 genomes]
rs62088920	0.81[ASN][1000 genomes]
rs638578	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs667695	1.00[ASN][1000 genomes]
rs671339	1.00[ASN][1000 genomes]
rs677461	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs680478	1.00[ASN][1000 genomes]
rs681297	1.00[ASN][1000 genomes]
rs683319	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs694861	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7233160	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7234128	0.89[ASN][1000 genomes]
rs8088389	0.86[ASN][1000 genomes]
rs8090919	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9807577	0.90[ASN][1000 genomes]
rs9807604	1.00[ASN][1000 genomes]
rs9950583	0.89[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	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv543644	chr18:9576145-9612516	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr18:9553800-9613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:9581400-9609200	Weak transcription	Pancreas	Pancrea
4	chr18:9588600-9612400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr18:9589000-9608800	Weak transcription	Thymus	Thymus
6	chr18:9589000-9609200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr18:9589000-9611000	Weak transcription	Lung	lung
8	chr18:9594200-9609200	Weak transcription	Aorta	Aorta
9	chr18:9594200-9613600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr18:9595200-9612000	Weak transcription	Esophagus	oesophagus
11	chr18:9595400-9608800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr18:9596000-9605800	Weak transcription	Hela-S3	cervix
13	chr18:9596000-9611000	Weak transcription	Gastric	stomach
14	chr18:9597000-9608800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr18:9597200-9611000	Weak transcription	NH-A	brain
16	chr18:9597400-9608000	Weak transcription	Osteobl	bone
17	chr18:9597400-9609200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr18:9597400-9613200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr18:9597600-9606000	Weak transcription	HUVEC	blood vessel
20	chr18:9597600-9609200	Weak transcription	Ovary	ovary
21	chr18:9598000-9612600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr18:9600200-9609400	Weak transcription	HSMM	muscle
23	chr18:9600800-9608400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr18:9601000-9605800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr18:9601000-9608200	Weak transcription	Stomach Mucosa	stomach
26	chr18:9601200-9608200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr18:9601200-9608400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr18:9601200-9608400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr18:9601400-9605400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr18:9601400-9608200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr18:9601400-9608200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr18:9601400-9608400	Weak transcription	NHLF	lung
33	chr18:9601400-9609200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr18:9601400-9610800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr18:9601600-9608200	Weak transcription	Fetal Intestine Small	intestine
36	chr18:9601600-9610800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr18:9601800-9609200	Weak transcription	Fetal Muscle Leg	muscle
38	chr18:9601800-9610400	Weak transcription	Fetal Stomach	stomach
39	chr18:9601800-9612200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr18:9602000-9605600	Weak transcription	A549	lung
41	chr18:9602200-9605600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr18:9602200-9606800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr18:9602200-9608400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr18:9602400-9608400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr18:9603000-9608200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr18:9603200-9609200	Weak transcription	Dnd41	blood
47	chr18:9603200-9610800	Weak transcription	Placenta	Placenta
48	chr18:9603200-9611000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr18:9603400-9609000	Weak transcription	Fetal Thymus	thymus
50	chr18:9603600-9611000	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links