Variant report

Variant	rs2070531
Chromosome Location	chr21:40194216-40194217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40193537..40196010-chr21:40225779..40228010,2	MCF-7	breast:
2	chr21:40191844..40194526-chr21:40280639..40282336,2	MCF-7	breast:
3	chr21:40193849..40196646-chr21:40227112..40228777,2	K562	blood:
4	chr21:40193156..40195802-chr21:40196323..40199129,2	K562	blood:
5	chr17:49243355..49244142-chr21:40193845..40194354,2	Hela-S3	cervix:
6	chr21:40194153..40196064-chr21:40203698..40205702,2	K562	blood:

Variant related genes	Relation type
ENSG00000243678	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1000844	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1009121	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1051420	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1051475	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051476	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10854389	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11088449	0.88[CEU][hapmap]
rs11088450	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11088451	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11088452	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11088453	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11088454	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1123350	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11254	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11701191	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11701500	0.82[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11702403	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12481740	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs12482470	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12483746	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12627283	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13046853	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13047133	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13047537	0.90[ASN][1000 genomes]
rs13047745	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13048035	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13050340	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1571707	0.94[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs2142035	0.82[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2283639	0.81[CEU][hapmap]
rs2836683	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836684	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836685	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836686	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836687	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836688	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836689	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836690	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836691	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836692	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836693	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836694	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836710	0.94[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2836711	0.82[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs6517481	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7276961	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7282444	0.82[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7282723	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762386	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762387	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9941892	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs998855	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2070531	PCP4	cis	cerebellum	SCAN
rs2070531	MX1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40180200-40198400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr21:40181800-40197000	Strong transcription	Fetal Thymus	thymus
3	chr21:40182000-40196600	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr21:40183000-40196600	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr21:40183600-40196800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr21:40183800-40196800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:40184000-40196800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr21:40184400-40196800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr21:40184600-40195000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr21:40184600-40196000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr21:40184800-40195200	Strong transcription	Ovary	ovary
12	chr21:40184800-40196600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr21:40184800-40196800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr21:40185000-40196600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr21:40185000-40196600	Strong transcription	K562	blood
16	chr21:40185000-40197000	Strong transcription	Thymus	Thymus
17	chr21:40185200-40196600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr21:40185600-40195200	Weak transcription	Fetal Brain Female	brain
19	chr21:40185600-40195200	Strong transcription	GM12878-XiMat	blood
20	chr21:40186000-40197600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr21:40186200-40195800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
22	chr21:40186200-40196400	Strong transcription	Primary B cells from cord blood	blood
23	chr21:40186200-40197000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr21:40186400-40194400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr21:40186400-40195200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr21:40186400-40195200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr21:40186600-40194800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr21:40186600-40196600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr21:40186600-40196800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr21:40186800-40196600	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr21:40186800-40196600	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr21:40186800-40196800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr21:40187000-40195200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr21:40187000-40196800	Genic enhancers	Rectal Mucosa Donor 31	rectum
35	chr21:40187000-40197400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr21:40187000-40197400	Strong transcription	Dnd41	blood
37	chr21:40188200-40196800	Strong transcription	Primary T cells from cord blood	blood
38	chr21:40188400-40195200	Strong transcription	Brain Substantia Nigra	brain
39	chr21:40188400-40195800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr21:40188400-40196200	Genic enhancers	Duodenum Mucosa	Duodenum
41	chr21:40188400-40196600	Strong transcription	Pancreas	Pancrea
42	chr21:40188800-40195200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr21:40188800-40196200	Genic enhancers	Rectal Mucosa Donor 29	rectum
44	chr21:40189200-40194800	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr21:40189400-40195200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr21:40189400-40195200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr21:40189400-40196000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr21:40189400-40196000	Genic enhancers	Placenta	Placenta
49	chr21:40189400-40196200	Genic enhancers	NHLF	lung
50	chr21:40189800-40194600	Strong transcription	HUVEC	blood vessel

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