Variant report

Variant	rs11893601
Chromosome Location	chr2:98314909-98314910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:98314807..98317005-chr2:98364935..98367106,2	K562	blood:
2	chr2:98313545..98315394-chr2:98316624..98319251,2	MCF-7	breast:
3	chr2:98260883..98263818-chr2:98313371..98315126,2	MCF-7	breast:
4	chr2:98312481..98316233-chr2:98322802..98326765,3	K562	blood:
5	chr2:98278086..98281780-chr2:98311810..98315713,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135940	Chromatin interaction
ENSG00000201806	Chromatin interaction
ENSG00000228486	Chromatin interaction
ENSG00000115073	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1020396	0.81[CHB][hapmap]
rs1042705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10496323	0.81[CHB][hapmap]
rs11123849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11680855	0.81[CHB][hapmap]
rs11894651	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12991969	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13001139	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13001728	0.81[CEU][hapmap]
rs13003963	0.90[ASN][1000 genomes]
rs13009163	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13034349	0.81[CHB][hapmap]
rs1375436	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1463174	0.81[CHB][hapmap]
rs1470625	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1550995	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1823324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2053824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2167007	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276644	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276645	0.81[CHB][hapmap]
rs2290124	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3474	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6542980	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs873886	0.95[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv874696	chr2:98309882-98362907	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11893601	ZAP70	cis	Nerve Tibial	GTEx
rs11893601	CNNM3	cis	cerebellum	SCAN
rs11893601	ANKRD36B	cis	lung	GTEx
rs11893601	ANKRD36B	cis	Nerve Tibial	GTEx
rs11893601	ZAP70	cis	cerebellum	SCAN
rs11893601	INPP4A	cis	cerebellum	SCAN
rs11893601		cis	Lymphoblastoid	GTEx
rs11893601	ANKRD36B	cis	cerebellum	SCAN
rs11893601	ANKRD36B	cis	Thyroid	GTEx
rs11893601	ACTR1B	cis	cerebellum	SCAN
rs11893601	ANKRD36B	cis	Artery Aorta	GTEx
rs11893601	ANKRD36B	cis	Artery Tibial	GTEx
rs11893601	ANKRD39	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98281000-98323800	Weak transcription	Gastric	stomach
2	chr2:98292200-98317800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:98306000-98322400	Weak transcription	Fetal Stomach	stomach
4	chr2:98308200-98316400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:98308400-98317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:98309400-98317800	Weak transcription	HSMM	muscle
7	chr2:98312800-98324600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:98313800-98315000	Weak transcription	Hela-S3	cervix
9	chr2:98313800-98316400	Weak transcription	Fetal Thymus	thymus
10	chr2:98313800-98316400	Weak transcription	HepG2	liver
11	chr2:98313800-98316400	Weak transcription	K562	blood
12	chr2:98313800-98316600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:98313800-98316600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:98313800-98317400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:98313800-98318000	Weak transcription	NHDF-Ad	bronchial
16	chr2:98313800-98318200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:98313800-98318400	Weak transcription	GM12878-XiMat	blood
18	chr2:98314000-98316400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:98314000-98316400	Weak transcription	Dnd41	blood
20	chr2:98314000-98316600	Weak transcription	Brain Anterior Caudate	brain
21	chr2:98314000-98318200	Weak transcription	Osteobl	bone
22	chr2:98314400-98315800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:98314800-98315200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links