Variant report

Variant	rs10488838
Chromosome Location	chr4:2881335-2881336
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2879534..2882793-chr4:2935370..2940285,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109736	Chromatin interaction
ENSG00000249673	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1034400	1.00[ASN][1000 genomes]
rs1263331	1.00[ASN][1000 genomes]
rs1574473	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843169	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843451	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843454	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843481	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843535	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843539	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843553	1.00[ASN][1000 genomes]
rs16843596	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005451	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857845	1.00[ASN][1000 genomes]
rs34120252	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34241425	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34550139	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34585460	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34743278	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34745961	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34945392	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35445752	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35508581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35893718	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35913891	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36038921	1.00[ASN][1000 genomes]
rs41528047	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4741	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4969	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56975682	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57155428	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57174035	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57557041	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57763208	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58059873	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58132256	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58196520	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58731679	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58758786	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58928665	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59426248	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59786983	1.00[ASN][1000 genomes]
rs59790260	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59798370	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60169711	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61117606	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61339714	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	esv3383963	chr4:2877954-2882252	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2870200-2914000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:2870600-2886000	Weak transcription	Fetal Brain Male	brain
3	chr4:2871000-2885800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:2871200-2881600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:2871200-2886000	Weak transcription	Aorta	Aorta
6	chr4:2871200-2896000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:2871200-2900600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:2872200-2890800	Weak transcription	A549	lung
9	chr4:2874000-2883600	Weak transcription	NH-A	brain
10	chr4:2874000-2887000	Weak transcription	Fetal Heart	heart
11	chr4:2874200-2900000	Weak transcription	Hela-S3	cervix
12	chr4:2875400-2886000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:2875800-2884200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:2876000-2881800	Strong transcription	Fetal Intestine Small	intestine
15	chr4:2876000-2884000	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:2876000-2885800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:2876000-2886000	Weak transcription	Colonic Mucosa	Colon
18	chr4:2876000-2886600	Weak transcription	Stomach Mucosa	stomach
19	chr4:2876400-2891600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:2876600-2882600	Strong transcription	Fetal Stomach	stomach
21	chr4:2876600-2889600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr4:2876800-2881800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:2876800-2889000	Strong transcription	GM12878-XiMat	blood
25	chr4:2876800-2889400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr4:2876800-2891800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:2877000-2882000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:2877000-2882200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr4:2877000-2883600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:2877000-2883800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:2877000-2886000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:2877000-2889800	Strong transcription	Dnd41	blood
33	chr4:2877200-2882000	Strong transcription	Brain Germinal Matrix	brain
34	chr4:2877200-2882200	Strong transcription	Fetal Muscle Leg	muscle
35	chr4:2877200-2886200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:2877200-2891800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:2877200-2919400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:2877400-2882000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:2877400-2882000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:2877400-2882000	Strong transcription	Placenta	Placenta
41	chr4:2877400-2882000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:2877400-2882000	Strong transcription	HepG2	liver
43	chr4:2877400-2882200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:2877400-2882400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr4:2877400-2882400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:2877400-2882400	Strong transcription	Fetal Intestine Large	intestine
47	chr4:2877400-2882400	Strong transcription	Fetal Lung	lung
48	chr4:2877400-2884000	Weak transcription	Small Intestine	intestine
49	chr4:2877400-2886200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:2877400-2889600	Strong transcription	Liver	Liver

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