Variant report

Variant	rs2236442
Chromosome Location	chr21:46271460-46271461
allele	C/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46265002..46266574-chr21:46269754..46272322,2	MCF-7	breast:
2	chr21:46244628..46247469-chr21:46269469..46271474,2	MCF-7	breast:
3	chr21:46271436..46274134-chr21:46295574..46298347,2	K562	blood:
4	chr21:46238241..46240355-chr21:46270733..46272763,2	K562	blood:
5	chr21:46270896..46276947-chr21:46277140..46283214,10	K562	blood:
6	chr21:46269227..46272682-chr21:46358261..46360343,3	K562	blood:
7	chr21:46227674..46230605-chr21:46271074..46273395,2	MCF-7	breast:
8	chr21:46256405..46259532-chr21:46270974..46273137,3	K562	blood:
9	chr21:46264380..46268999-chr21:46269204..46276124,8	K562	blood:
10	chr21:46270971..46273978-chr21:46365251..46368818,3	MCF-7	breast:
11	chr21:46253846..46255702-chr21:46270188..46272414,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160256	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000184900	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1054220	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13050968	0.81[ASN][1000 genomes]
rs13052639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2117340	0.81[ASN][1000 genomes]
rs2117341	0.81[ASN][1000 genomes]
rs2838711	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838712	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2838713	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35199002	1.00[ASN][1000 genomes]
rs35424519	1.00[ASN][1000 genomes]
rs35432315	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35846107	1.00[ASN][1000 genomes]
rs3810586	0.81[ASN][1000 genomes]
rs7279563	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv459298	chr21:46223847-46277968	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv587813	chr21:46223847-46277968	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv913963	chr21:46223847-46277968	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv913964	chr21:46223847-46298869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv913962	chr21:46223847-46321172	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv913965	chr21:46223847-46321172	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1058550	chr21:46227163-46317934	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv913967	chr21:46249752-46279505	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv913968	chr21:46249752-46301008	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv1060233	chr21:46254075-46323401	Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv1056513	chr21:46254075-46442759	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2236442	PTTG1IP	cis	Heart Left Ventricle	GTEx
rs2236442	ENSG00000183255	cis	multi-tissue	Pritchard
rs2236442	PTTG1IP	cis	Artery Tibial	GTEx
rs2236442	PTTG1IP	cis	Artery Aorta	GTEx
rs2236442	PTTG1IP	cis	lung	GTEx
rs2236442	PTTG1IP	Cis_1M	lymphoblastoid	RTeQTL
rs2236442	PTTG1IP	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46266600-46278800	Weak transcription	Fetal Kidney	kidney
2	chr21:46267200-46274000	Weak transcription	Small Intestine	intestine
3	chr21:46267400-46271600	Genic enhancers	Fetal Intestine Small	intestine
4	chr21:46267400-46285200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr21:46267400-46286600	Strong transcription	Fetal Stomach	stomach
6	chr21:46267600-46273000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:46267600-46277000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr21:46267600-46280600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr21:46267600-46287000	Strong transcription	Brain Germinal Matrix	brain
10	chr21:46267800-46273400	Weak transcription	Right Atrium	heart
11	chr21:46267800-46273600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr21:46268000-46273000	Strong transcription	Placenta	Placenta
13	chr21:46268000-46278800	Strong transcription	Stomach Smooth Muscle	stomach
14	chr21:46268000-46281200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr21:46268200-46274000	Strong transcription	Fetal Muscle Trunk	muscle
16	chr21:46268200-46278400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr21:46268200-46281200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr21:46268200-46285800	Strong transcription	Fetal Muscle Leg	muscle
19	chr21:46268600-46271600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr21:46268600-46271600	Strong transcription	Brain Cingulate Gyrus	brain
21	chr21:46268600-46271600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr21:46268600-46272000	Strong transcription	Brain Substantia Nigra	brain
23	chr21:46268600-46272200	Genic enhancers	Duodenum Mucosa	Duodenum
24	chr21:46268600-46272200	Strong transcription	Left Ventricle	heart
25	chr21:46268600-46273400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr21:46268600-46273600	Strong transcription	Spleen	Spleen
27	chr21:46268600-46273800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr21:46268600-46274400	Genic enhancers	Fetal Intestine Large	intestine
29	chr21:46268600-46276600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr21:46268600-46276600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr21:46268600-46277600	Strong transcription	Brain Hippocampus Middle	brain
32	chr21:46268600-46277600	Strong transcription	HMEC	breast
33	chr21:46268600-46278200	Strong transcription	Adipose Nuclei	Adipose
34	chr21:46268600-46278400	Strong transcription	Lung	lung
35	chr21:46268600-46278600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr21:46268600-46279800	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr21:46268600-46280600	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr21:46268600-46280600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr21:46268600-46281800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr21:46268600-46281800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr21:46268600-46282000	Strong transcription	Fetal Brain Female	brain
42	chr21:46268600-46285200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr21:46268600-46285200	Strong transcription	Osteobl	bone
44	chr21:46268600-46285400	Strong transcription	Thymus	Thymus
45	chr21:46268600-46285400	Strong transcription	HUVEC	blood vessel
46	chr21:46268600-46285800	Strong transcription	Liver	Liver
47	chr21:46268600-46286000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr21:46268600-46286600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr21:46268800-46271600	Strong transcription	Brain Anterior Caudate	brain
50	chr21:46268800-46271600	Strong transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links