Variant report

Variant	rs13120798
Chromosome Location	chr4:119708441-119708442
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	chr4:119706080..119708529-chr4:119755979..119757565,2	MCF-7	breast:
2	chr4:119708422..119711280-chr4:119731156..119733832,2	K562	blood:

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10011672	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10014208	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10470914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10518322	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518324	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098449	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11098450	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11722833	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11730993	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11736024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12500272	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12505513	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12506295	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12506576	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12509236	0.87[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12509654	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs12649666	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13109947	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13109966	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13114964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13128195	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17050423	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303512	0.86[CHB][hapmap]
rs2303513	0.82[CEU][hapmap]
rs298977	0.86[CEU][hapmap]
rs298980	0.86[CEU][hapmap]
rs298981	0.86[CEU][hapmap]
rs298989	0.86[AMR][1000 genomes]
rs298990	0.83[CEU][hapmap];0.86[AMR][1000 genomes]
rs34384498	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34616305	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34730066	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35868882	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775836	0.80[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4833592	0.80[CHB][hapmap]
rs4834699	0.87[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58450672	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs67175714	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7676832	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs960738	0.81[JPT][hapmap]
rs960739	0.91[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs9997799	0.81[AMR][1000 genomes];0.99[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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
2	chr4:119678600-119717400	Weak transcription	Esophagus	oesophagus
3	chr4:119679000-119717600	Weak transcription	Colonic Mucosa	Colon
4	chr4:119687600-119711800	Weak transcription	Stomach Mucosa	stomach
5	chr4:119688600-119710000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:119688600-119712800	Weak transcription	Gastric	stomach
7	chr4:119688600-119715800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:119688600-119717400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:119688600-119717400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:119688600-119732600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:119688800-119716800	Weak transcription	Fetal Kidney	kidney
12	chr4:119689400-119709000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr4:119689400-119716200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:119689400-119716600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:119689400-119716800	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:119689600-119709400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:119689600-119717600	Weak transcription	K562	blood
18	chr4:119689800-119708800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:119690000-119717600	Weak transcription	Primary T cells from cord blood	blood
20	chr4:119694000-119715000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:119694000-119717400	Weak transcription	Ovary	ovary
22	chr4:119694400-119716600	Weak transcription	Aorta	Aorta
23	chr4:119695000-119710000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:119695000-119717600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:119696400-119715600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:119696800-119717400	Weak transcription	Spleen	Spleen
27	chr4:119698000-119709400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:119698200-119712200	Weak transcription	Adipose Nuclei	Adipose
29	chr4:119702600-119717600	Weak transcription	Fetal Brain Male	brain
30	chr4:119703000-119711000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:119703400-119732200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr4:119703800-119738200	Strong transcription	Placenta	Placenta
33	chr4:119704000-119710000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:119704200-119712600	Strong transcription	NH-A	brain
35	chr4:119704200-119713000	Weak transcription	Lung	lung
36	chr4:119704200-119740000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:119704400-119714000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:119704400-119717600	Weak transcription	Pancreas	Pancrea
39	chr4:119704600-119708600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:119704600-119708600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:119704600-119708600	Weak transcription	Fetal Intestine Small	intestine
42	chr4:119704600-119709000	Weak transcription	Fetal Intestine Large	intestine
43	chr4:119704600-119715600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:119704600-119716400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr4:119704600-119717600	Weak transcription	Small Intestine	intestine
46	chr4:119704800-119710000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr4:119704800-119712400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr4:119704800-119713600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:119704800-119715600	Weak transcription	Primary B cells from cord blood	blood
50	chr4:119704800-119735200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links