Variant report

Variant	rs11675404
Chromosome Location	chr2:172737981-172737982
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172733666..172736692-chr2:172737293..172740256,4	K562	blood:
2	chr2:172724899..172727363-chr2:172737515..172740249,2	K562	blood:
3	chr2:172737244..172739400-chr2:172984997..172987788,2	MCF-7	breast:
4	chr2:172733649..172740490-chr2:172749209..172752081,6	MCF-7	breast:
5	chr2:172736226..172738889-chr2:172742380..172745045,2	K562	blood:
6	chr2:172737251..172741632-chr2:172744127..172746151,4	K562	blood:
7	chr2:172729602..172731733-chr2:172737376..172738895,2	K562	blood:
8	chr2:172708386..172710884-chr2:172736150..172738509,2	K562	blood:
9	chr2:172736755..172739863-chr2:172746964..172750897,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11673831	0.83[AMR][1000 genomes]
rs11678018	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11681005	0.82[ASW][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap]
rs11691301	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11695630	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes]
rs12991441	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12996935	0.82[ASW][hapmap]
rs13016580	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13021138	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13024662	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1554259	0.80[AMR][1000 genomes]
rs17427311	0.84[AFR][1000 genomes]
rs17427473	1.00[ASW][hapmap];0.83[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17499306	0.82[CEU][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap]
rs17499502	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs17848721	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1996424	0.82[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2138349	1.00[ASW][hapmap];0.83[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2357062	0.84[AFR][1000 genomes]
rs34108287	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34137430	0.83[AMR][1000 genomes]
rs34221876	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34632749	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs34962243	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3770459	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4581870	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs62182397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62182402	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62182403	0.87[ASN][1000 genomes]
rs62182435	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62182443	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62183760	0.81[AMR][1000 genomes]
rs62183768	0.83[AMR][1000 genomes]
rs62183773	0.82[AMR][1000 genomes]
rs62184174	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6718013	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs6737308	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs74173119	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7584187	0.84[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv583611	chr2:172683481-172750257	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv1006214	chr2:172691689-172754296	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv536036	chr2:172691689-172754296	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11675404	DYNC1I2	cis	cerebellum	SCAN
rs11675404	MAP1D	cis	parietal	SCAN
rs11675404	B3GALT1	cis	cerebellum	SCAN
rs11675404	SLC25A12	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172690200-172750200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:172691400-172738600	Weak transcription	Esophagus	oesophagus
3	chr2:172709600-172749600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:172709600-172749600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:172710800-172747800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:172711600-172740000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:172712200-172749200	Weak transcription	Hela-S3	cervix
8	chr2:172712400-172738200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:172721200-172749600	Weak transcription	Thymus	Thymus
10	chr2:172724000-172749600	Weak transcription	Small Intestine	intestine
11	chr2:172724800-172749600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:172725400-172749800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:172725800-172749600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:172727800-172738600	Weak transcription	Dnd41	blood
15	chr2:172731400-172746400	Weak transcription	Fetal Lung	lung
16	chr2:172731600-172749600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:172731800-172740600	Weak transcription	Fetal Stomach	stomach
18	chr2:172731800-172746400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:172732000-172738600	Weak transcription	Primary T cells from cord blood	blood
20	chr2:172732000-172746000	Weak transcription	Fetal Brain Female	brain
21	chr2:172732000-172746400	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:172732000-172746400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:172732000-172746600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:172732000-172748800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr2:172732000-172749400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:172732000-172749400	Weak transcription	A549	lung
27	chr2:172732000-172749600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:172732000-172749800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:172732000-172749800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr2:172732000-172750000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:172732200-172746400	Weak transcription	Primary B cells from cord blood	blood
32	chr2:172732200-172749600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:172732400-172749600	Weak transcription	Fetal Kidney	kidney
34	chr2:172732400-172749800	Weak transcription	Fetal Thymus	thymus
35	chr2:172732600-172747000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:172733000-172746400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:172733000-172749200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:172733000-172749400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:172735200-172749600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:172735400-172746600	Weak transcription	HSMM	muscle
41	chr2:172735400-172748200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:172735400-172748400	Weak transcription	Brain Anterior Caudate	brain
43	chr2:172735400-172749400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:172735400-172749400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:172735400-172749400	Weak transcription	Brain Hippocampus Middle	brain
46	chr2:172735400-172749600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:172735400-172749600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:172735400-172749600	Weak transcription	NHDF-Ad	bronchial
49	chr2:172735400-172749600	Weak transcription	NHEK	skin
50	chr2:172735600-172738200	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links