Variant report

Variant	rs663956
Chromosome Location	chr21:40970184-40970185
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40963714..40965931-chr21:40968819..40971403,2	K562	blood:
2	chr21:40968353..40970588-chr21:40974618..40978683,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C21orf88-1	chr21:40969031-40972206	NONHSAT082200

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs502544	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508141	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535457	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs536444	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs599163	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv34779	chr21:40884871-40977473	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS 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	15 gene(s)	inside rSNPs	diseases
5	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs663956	PCP4	cis	cerebellum	SCAN
rs663956	RIPK4	cis	parietal	SCAN
rs663956	BRWD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40965600-40976400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr21:40967800-40974000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:40969200-40970200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr21:40969200-40970400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr21:40969200-40970400	Enhancers	Spleen	Spleen
6	chr21:40969200-40970600	Enhancers	Fetal Heart	heart
7	chr21:40969400-40970200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr21:40969400-40970400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr21:40969600-40970200	Enhancers	Fetal Stomach	stomach
10	chr21:40969600-40970400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr21:40969800-40970200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr21:40969800-40970200	Enhancers	Fetal Muscle Trunk	muscle
13	chr21:40969800-40970400	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr21:40970000-40970200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr21:40970000-40970200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr21:40970000-40970200	Enhancers	H9 Cell Line	embryonic stem cell
17	chr21:40970000-40970400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr21:40970000-40970400	Enhancers	Fetal Thymus	thymus
19	chr21:40970000-40970600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:40970000-40972400	Weak transcription	Brain Hippocampus Middle	brain
21	chr21:40970000-40973200	Weak transcription	Brain Substantia Nigra	brain

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