Variant report

Variant	rs235317
Chromosome Location	chr21:46275047-46275048
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46219335..46222066-chr21:46273401..46276470,3	K562	blood:
2	chr21:46266013..46268902-chr21:46273662..46275301,2	MCF-7	breast:
3	chr21:46235456..46240061-chr21:46274213..46277506,6	K562	blood:
4	chr21:46273736..46276118-chr21:46318911..46321245,2	K562	blood:
5	chr21:46236941..46239715-chr21:46273416..46275344,2	MCF-7	breast:
6	chr21:46238188..46240407-chr21:46273187..46276498,3	K562	blood:
7	chr21:46264289..46271339-chr21:46271625..46276632,16	K562	blood:
8	chr21:46272154..46279111-chr21:46289852..46295619,12	K562	blood:
9	chr21:46274377..46276734-chr21:46492349..46494888,2	K562	blood:
10	chr21:46218586..46220158-chr21:46274953..46276818,2	K562	blood:
11	chr21:46274218..46276249-chr21:46318911..46322162,3	K562	blood:
12	chr21:46272684..46279612-chr21:46286573..46290125,9	K562	blood:
13	chr21:46270896..46276947-chr21:46277140..46283214,10	K562	blood:
14	chr21:46273548..46279979-chr21:46290137..46294261,8	K562	blood:
15	chr21:46272890..46275877-chr21:46493388..46495047,2	K562	blood:
16	chr21:46274509..46277434-chr21:46346749..46348631,2	MCF-7	breast:
17	chr21:46254101..46256676-chr21:46273312..46275198,2	K562	blood:
18	chr21:46264380..46268999-chr21:46269204..46276124,8	K562	blood:
19	chr17:56708400..56710403-chr21:46274610..46277048,2	MCF-7	breast:
20	chr21:46235456..46237470-chr21:46274330..46277506,4	K562	blood:
21	chr21:46274905..46276457-chr21:46283894..46285475,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184900	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000235374	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13051895	0.80[JPT][hapmap]
rs235305	0.90[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap]
rs235370	0.85[YRI][hapmap]
rs441019	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4818738	0.84[JPT][hapmap]
rs873317	0.84[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs235317	KRTAP10-11	cis	cerebellum	SCAN
rs235317	PLAC4	cis	cerebellum	SCAN
rs235317	COL18A1	cis	parietal	SCAN
rs235317	PTTG1IP	Cis_1M	lymphoblastoid	RTeQTL

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	chr21:46267400-46285200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr21:46267400-46286600	Strong transcription	Fetal Stomach	stomach
4	chr21:46267600-46277000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr21:46267600-46280600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr21:46267600-46287000	Strong transcription	Brain Germinal Matrix	brain
7	chr21:46268000-46278800	Strong transcription	Stomach Smooth Muscle	stomach
8	chr21:46268000-46281200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr21:46268200-46278400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:46268200-46281200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr21:46268200-46285800	Strong transcription	Fetal Muscle Leg	muscle
12	chr21:46268600-46276600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr21:46268600-46276600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr21:46268600-46277600	Strong transcription	Brain Hippocampus Middle	brain
15	chr21:46268600-46277600	Strong transcription	HMEC	breast
16	chr21:46268600-46278200	Strong transcription	Adipose Nuclei	Adipose
17	chr21:46268600-46278400	Strong transcription	Lung	lung
18	chr21:46268600-46278600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr21:46268600-46279800	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr21:46268600-46280600	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr21:46268600-46280600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr21:46268600-46281800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr21:46268600-46281800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr21:46268600-46282000	Strong transcription	Fetal Brain Female	brain
25	chr21:46268600-46285200	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr21:46268600-46285200	Strong transcription	Osteobl	bone
27	chr21:46268600-46285400	Strong transcription	Thymus	Thymus
28	chr21:46268600-46285400	Strong transcription	HUVEC	blood vessel
29	chr21:46268600-46285800	Strong transcription	Liver	Liver
30	chr21:46268600-46286000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr21:46268600-46286600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr21:46268800-46276400	Strong transcription	Brain Angular Gyrus	brain
33	chr21:46268800-46276600	Strong transcription	Aorta	Aorta
34	chr21:46268800-46276800	Strong transcription	GM12878-XiMat	blood
35	chr21:46268800-46277000	Strong transcription	Colon Smooth Muscle	Colon
36	chr21:46268800-46279800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr21:46268800-46285200	Strong transcription	Dnd41	blood
38	chr21:46268800-46285200	Strong transcription	NHLF	lung
39	chr21:46268800-46285400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr21:46268800-46286600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr21:46268800-46286600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr21:46268800-46286600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr21:46269000-46277400	Strong transcription	HSMM	muscle
44	chr21:46269200-46276000	Strong transcription	NH-A	brain
45	chr21:46269200-46279800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr21:46269400-46280800	Strong transcription	Hela-S3	cervix
47	chr21:46269400-46285800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr21:46269600-46281600	Strong transcription	Pancreas	Pancrea
49	chr21:46269800-46275800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
50	chr21:46270000-46278600	Weak transcription	Fetal Brain Male	brain

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