Variant report

Variant	rs8134327
Chromosome Location	chr21:17103199-17103200
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	chr21:17101236..17104015-chr21:17196099..17198458,3	MCF-7	breast:
2	chr21:17099652..17105374-chr21:17196149..17200245,6	MCF-7	breast:
3	chr21:17102987..17104761-chr21:17143817..17145697,2	K562	blood:
4	chr21:17064915..17067118-chr21:17101217..17104804,3	MCF-7	breast:
5	chr1:144533860..144534669-chr21:17102967..17103936,2	Hela-S3	cervix:
6	chr21:17102586..17104212-chr21:17132608..17135141,2	K562	blood:
7	chr21:17079550..17081634-chr21:17101174..17103507,3	MCF-7	breast:
8	chr21:17064242..17066910-chr21:17102295..17103877,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000155313	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000238591	Chromatin interaction
ENSG00000221497	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10482876	0.91[CEU][hapmap]
rs11910884	0.90[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs11911814	0.85[AMR][1000 genomes]
rs13347185	0.80[AFR][1000 genomes]
rs1543299	0.82[CEU][hapmap]
rs17241416	0.91[CEU][hapmap]
rs17241423	0.89[CEU][hapmap]
rs17241430	0.91[CEU][hapmap]
rs17241444	0.91[CEU][hapmap]
rs17307120	0.91[CEU][hapmap]
rs17307176	0.91[CEU][hapmap]
rs1989381	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2026853	0.94[ASW][hapmap];0.91[CEU][hapmap];0.81[CHB][hapmap];0.96[YRI][hapmap]
rs2205585	0.84[AFR][1000 genomes]
rs2223176	0.84[AFR][1000 genomes]
rs2242676	0.91[CEU][hapmap]
rs2245574	0.82[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap]
rs2823453	0.84[CEU][hapmap]
rs2823455	0.82[CEU][hapmap]
rs2823457	0.84[CEU][hapmap]
rs2823462	0.91[CEU][hapmap]
rs2823463	0.91[CEU][hapmap]
rs2823467	0.86[AFR][1000 genomes]
rs2823469	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2823470	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2823471	0.91[CEU][hapmap]
rs2823472	0.91[CEU][hapmap];0.82[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2823473	0.82[AFR][1000 genomes]
rs2823476	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2823477	0.86[YRI][hapmap]
rs2823478	0.91[CEU][hapmap]
rs2823482	0.89[ASW][hapmap];0.82[CHB][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2823487	0.86[YRI][hapmap]
rs2823489	0.91[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823491	0.91[CEU][hapmap]
rs2823493	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs2823495	0.81[AFR][1000 genomes]
rs2823496	0.84[AFR][1000 genomes]
rs2823497	0.82[AFR][1000 genomes]
rs2823499	0.89[ASW][hapmap];0.91[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap]
rs2823500	0.91[CEU][hapmap];0.93[YRI][hapmap]
rs2823504	0.82[CEU][hapmap]
rs28627435	0.86[AFR][1000 genomes]
rs28725201	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28730511	0.81[AFR][1000 genomes]
rs3787577	0.91[CEU][hapmap]
rs6517609	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517611	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6517612	1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs6517613	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517648	1.00[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6517652	1.00[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs722887	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7277807	0.91[CEU][hapmap]
rs7277813	0.84[AFR][1000 genomes]
rs7278428	0.91[CEU][hapmap]
rs7279157	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7279170	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7281511	0.91[CEU][hapmap];0.90[YRI][hapmap]
rs7283707	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7283764	0.91[CEU][hapmap]
rs8127158	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8130607	1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs926612	1.00[MEX][hapmap]
rs9941829	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9974210	0.82[AFR][1000 genomes]
rs9977000	0.82[AFR][1000 genomes]
rs9981766	0.84[AFR][1000 genomes]
rs9982083	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9982479	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9983458	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762093	chr21:16948663-17145770	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1064683	chr21:16954570-17145758	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv459099	chr21:16956866-17145011	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv587076	chr21:16956866-17145011	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1062105	chr21:16956885-17141961	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544380	chr21:16956885-17141961	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1059500	chr21:16957752-17145758	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv2830057	chr21:16960590-17113148	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	esv3323481	chr21:17101106-17103654	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
10	esv3429322	chr21:17101431-17103829	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8134327	MSX1	trans	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17101400-17103400	Active TSS	Duodenum Mucosa	Duodenum
2	chr21:17101400-17103600	Active TSS	Brain Cingulate Gyrus	brain
3	chr21:17101400-17104000	Active TSS	Brain Anterior Caudate	brain
4	chr21:17101400-17104000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr21:17101600-17103400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr21:17101600-17103400	Active TSS	Brain Hippocampus Middle	brain
7	chr21:17101600-17103400	Active TSS	Fetal Brain Female	brain
8	chr21:17101600-17103400	Active TSS	Fetal Lung	lung
9	chr21:17101600-17103600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr21:17101600-17103600	Active TSS	Primary monocytes fromperipheralblood	blood
11	chr21:17101600-17103600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr21:17101600-17103600	Active TSS	Brain Germinal Matrix	brain
13	chr21:17101600-17103600	Active TSS	Brain Substantia Nigra	brain
14	chr21:17101600-17103600	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr21:17101600-17103600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr21:17101600-17104000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr21:17101600-17104200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr21:17101600-17104200	Active TSS	Fetal Intestine Large	intestine
19	chr21:17101600-17104600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr21:17101600-17104600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr21:17101600-17104600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr21:17101600-17104600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr21:17101600-17104800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr21:17101600-17104800	Active TSS	Colon Smooth Muscle	Colon
25	chr21:17101600-17105000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr21:17101600-17105000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr21:17101600-17105000	Active TSS	Fetal Intestine Small	intestine
28	chr21:17101600-17105000	Active TSS	NHDF-Ad	bronchial
29	chr21:17101600-17105200	Active TSS	H1 Cell Line	embryonic stem cell
30	chr21:17101600-17105200	Active TSS	Right Ventricle	heart
31	chr21:17101600-17105400	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr21:17101600-17105400	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr21:17101600-17105400	Active TSS	Stomach Smooth Muscle	stomach
34	chr21:17101600-17105600	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr21:17101600-17105800	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr21:17101600-17105800	Active TSS	K562	blood
37	chr21:17101800-17103200	Active TSS	Spleen	Spleen
38	chr21:17101800-17103400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr21:17101800-17103400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr21:17101800-17103400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr21:17101800-17103400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr21:17101800-17103400	Active TSS	Gastric	stomach
43	chr21:17101800-17103600	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr21:17101800-17103800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr21:17101800-17103800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr21:17101800-17103800	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr21:17101800-17103800	Active TSS	Esophagus	oesophagus
48	chr21:17101800-17103800	Active TSS	Left Ventricle	heart
49	chr21:17101800-17103800	Active TSS	Lung	lung
50	chr21:17101800-17103800	Active TSS	Sigmoid Colon	Sigmoid Colon

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