Variant report

Variant	rs235310
Chromosome Location	chr21:46268361-46268362
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46266013..46268902-chr21:46273662..46275301,2	MCF-7	breast:
2	chr21:46264289..46271339-chr21:46271625..46276632,16	K562	blood:
3	chr21:46267660..46269826-chr21:46493577..46495142,2	K562	blood:
4	chr21:46221083..46222919-chr21:46268127..46270057,2	MCF-7	breast:
5	chr21:46236130..46239998-chr21:46264824..46268393,7	MCF-7	breast:
6	chr21:46266846..46268611-chr21:46268857..46270465,2	MCF-7	breast:
7	chr21:46267198..46269183-chr21:46277821..46280408,2	K562	blood:
8	chr21:46264380..46268999-chr21:46269204..46276124,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184900	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000236519	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2838724	0.81[GIH][hapmap];0.81[JPT][hapmap]
rs381406	0.81[JPT][hapmap]
rs4818980	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs235310	C21orf125	cis	cerebellum	SCAN
rs235310	KRTAP10-11	cis	cerebellum	SCAN
rs235310	COL18A1	cis	parietal	SCAN
rs235310	KRTAP10-10	cis	parietal	SCAN
rs235310	PCBP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46264600-46268800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:46266000-46268600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr21:46266000-46268800	Weak transcription	Ovary	ovary
4	chr21:46266200-46268600	Enhancers	Fetal Intestine Large	intestine
5	chr21:46266200-46268800	Weak transcription	Psoas Muscle	Psoas
6	chr21:46266200-46269200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr21:46266400-46269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr21:46266400-46269200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr21:46266400-46269400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr21:46266600-46268600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr21:46266600-46268800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr21:46266600-46268800	Weak transcription	Primary T cells from cord blood	blood
13	chr21:46266600-46268800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr21:46266600-46269200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr21:46266600-46269200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr21:46266600-46278800	Weak transcription	Fetal Kidney	kidney
17	chr21:46266800-46268400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr21:46266800-46268600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr21:46266800-46268600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr21:46266800-46268600	Weak transcription	Thymus	Thymus
21	chr21:46266800-46268600	Weak transcription	NHEK	skin
22	chr21:46266800-46268800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr21:46266800-46268800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr21:46266800-46268800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr21:46266800-46268800	Weak transcription	Primary B cells from cord blood	blood
26	chr21:46266800-46268800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr21:46266800-46268800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr21:46266800-46268800	Weak transcription	Colon Smooth Muscle	Colon
29	chr21:46266800-46268800	Weak transcription	A549	lung
30	chr21:46266800-46268800	Weak transcription	GM12878-XiMat	blood
31	chr21:46266800-46269000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr21:46266800-46269200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr21:46266800-46269200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr21:46266800-46269200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr21:46266800-46269400	Weak transcription	Fetal Heart	heart
36	chr21:46266800-46269800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr21:46266800-46270400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr21:46267000-46268600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr21:46267000-46268600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr21:46267000-46268600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr21:46267000-46268600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr21:46267000-46268600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr21:46267000-46268600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr21:46267000-46268600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr21:46267000-46268600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr21:46267000-46268600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr21:46267000-46268600	Weak transcription	Brain Hippocampus Middle	brain
48	chr21:46267000-46268600	Weak transcription	Brain Substantia Nigra	brain
49	chr21:46267000-46268600	Weak transcription	Fetal Thymus	thymus
50	chr21:46267000-46268800	Weak transcription	Primary B cells from peripheral blood	blood

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