Variant report

Variant	rs2404001
Chromosome Location	chr21:17210838-17210839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:17210212..17212761-chr21:17213136..17214985,3	MCF-7	breast:
2	chr21:17204445..17206972-chr21:17210120..17212633,3	K562	blood:
3	chr21:17102373..17104701-chr21:17209803..17211415,2	K562	blood:

Variant related genes	Relation type
ENSG00000155313	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10482876	0.83[CEU][hapmap]
rs11910884	0.81[CEU][hapmap]
rs17241416	0.83[CEU][hapmap]
rs17241430	0.83[CEU][hapmap]
rs17241444	0.83[CEU][hapmap]
rs17307176	0.83[CEU][hapmap]
rs2026853	0.83[CEU][hapmap]
rs2242676	0.83[CEU][hapmap]
rs2823471	0.83[CEU][hapmap]
rs2823472	0.83[CEU][hapmap]
rs2823478	0.83[CEU][hapmap]
rs2823489	0.83[CEU][hapmap]
rs2823491	0.83[CEU][hapmap]
rs2823493	0.83[CEU][hapmap]
rs2823499	0.83[CEU][hapmap]
rs2823500	0.83[CEU][hapmap]
rs2823502	0.83[ASN][1000 genomes]
rs2823503	0.83[ASN][1000 genomes]
rs2823504	0.91[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs2823506	0.93[ASN][1000 genomes]
rs2823507	0.85[ASN][1000 genomes]
rs28469763	0.86[ASN][1000 genomes]
rs3787577	0.83[CEU][hapmap]
rs6517609	0.83[CEU][hapmap]
rs6517613	0.83[CEU][hapmap]
rs6517648	0.83[CEU][hapmap]
rs6517652	0.83[CEU][hapmap]
rs7281511	0.83[CEU][hapmap]
rs7283707	0.83[CEU][hapmap]
rs8127158	0.83[CEU][hapmap]
rs8127570	0.84[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	nsv834050	chr21:17146090-17348951	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1063035	chr21:17154222-17224344	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2404001	MSX1	trans	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17155200-17252800	Weak transcription	Fetal Brain Male	brain
2	chr21:17178400-17248200	Weak transcription	Esophagus	oesophagus
3	chr21:17178400-17252800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr21:17178800-17211400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr21:17182400-17227800	Weak transcription	Psoas Muscle	Psoas
6	chr21:17188000-17214000	Weak transcription	Gastric	stomach
7	chr21:17188000-17229400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr21:17188000-17240200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr21:17188200-17213400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr21:17188200-17246800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr21:17188400-17247200	Weak transcription	Ovary	ovary
12	chr21:17188400-17253200	Weak transcription	Fetal Brain Female	brain
13	chr21:17188600-17213400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr21:17188800-17247000	Weak transcription	Brain Germinal Matrix	brain
15	chr21:17188800-17252600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr21:17190200-17245400	Weak transcription	Lung	lung
17	chr21:17190200-17247200	Weak transcription	Pancreas	Pancrea
18	chr21:17190400-17247200	Weak transcription	Spleen	Spleen
19	chr21:17190400-17247400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr21:17191000-17227800	Weak transcription	Colonic Mucosa	Colon
21	chr21:17191800-17211600	Weak transcription	NH-A	brain
22	chr21:17191800-17212800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr21:17194200-17228000	Weak transcription	Small Intestine	intestine
24	chr21:17194800-17218000	Weak transcription	Hela-S3	cervix
25	chr21:17197200-17218400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr21:17198000-17214200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr21:17198000-17248000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr21:17199400-17218800	Weak transcription	Right Ventricle	heart
29	chr21:17199600-17213200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr21:17199800-17214200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr21:17199800-17246800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr21:17199800-17247200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr21:17200000-17211800	Weak transcription	NHEK	skin
34	chr21:17200000-17213400	Weak transcription	NHDF-Ad	bronchial
35	chr21:17200800-17245200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr21:17201200-17230200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr21:17201400-17245400	Weak transcription	Fetal Stomach	stomach
38	chr21:17204200-17213400	Weak transcription	NHLF	lung
39	chr21:17204400-17239000	Weak transcription	Brain Substantia Nigra	brain
40	chr21:17204400-17246400	Weak transcription	Brain Angular Gyrus	brain
41	chr21:17204400-17246800	Weak transcription	Brain Anterior Caudate	brain
42	chr21:17204600-17211200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr21:17204600-17213000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr21:17204600-17213600	Weak transcription	A549	lung
45	chr21:17204600-17214200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr21:17204600-17214800	Weak transcription	K562	blood
47	chr21:17204600-17219800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr21:17204600-17220000	Weak transcription	Thymus	Thymus
49	chr21:17204600-17229200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr21:17204600-17230200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links