Variant report

Variant	rs219781
Chromosome Location	chr21:37832621-37832622
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:37831208..37834228-chr21:37836709..37839908,3	MCF-7	breast:
2	chr21:37807939..37809702-chr21:37831962..37833487,2	MCF-7	breast:
3	chr21:37830343..37833071-chr21:37835621..37838183,2	K562	blood:
4	chr21:37801180..37804011-chr21:37832041..37834948,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHAF1B-2	chr21:37832588-37833050	ENSG00000233818.1

Variant related genes	Relation type
ENSG00000159261	Chromatin interaction
ENSG00000230479	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs16994103	1.00[ASN][1000 genomes]
rs2101437	1.00[ASN][1000 genomes]
rs219767	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219768	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219769	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219770	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219771	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219772	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219773	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219774	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219775	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219776	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219777	0.94[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219778	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219779	1.00[CEU][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219782	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219783	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219784	0.89[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219787	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs219788	0.83[CEU][hapmap]
rs219790	0.90[EUR][1000 genomes]
rs219791	0.89[EUR][1000 genomes]
rs2835343	1.00[ASN][1000 genomes]
rs2835363	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35692359	1.00[ASN][1000 genomes]
rs55801805	1.00[ASN][1000 genomes]
rs73902527	1.00[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	nsv834090	chr21:37812545-38009542	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv33286	chr21:37827016-37861556	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs219781	MRAP	cis	parietal	SCAN
rs219781	DSCR6	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:37810400-37833400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr21:37824800-37836800	Weak transcription	Right Atrium	heart
3	chr21:37825800-37833600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr21:37827200-37834000	Weak transcription	A549	lung
5	chr21:37827200-37837200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr21:37827400-37834000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr21:37827400-37836400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr21:37827400-37836800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr21:37827600-37834200	Weak transcription	Fetal Kidney	kidney
10	chr21:37827600-37834600	Weak transcription	Brain Anterior Caudate	brain
11	chr21:37827800-37834400	Weak transcription	Ovary	ovary
12	chr21:37829400-37833600	Weak transcription	Esophagus	oesophagus
13	chr21:37829800-37833600	Weak transcription	Gastric	stomach
14	chr21:37830000-37833800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr21:37831400-37833200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr21:37831600-37832800	Enhancers	HSMMtube	muscle
17	chr21:37831600-37833200	Enhancers	Pancreas	Pancrea
18	chr21:37831800-37833000	Enhancers	Lung	lung
19	chr21:37832000-37832800	Enhancers	NH-A	brain
20	chr21:37832000-37833000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr21:37832000-37833800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr21:37832200-37833200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr21:37832200-37833600	Weak transcription	Spleen	Spleen
24	chr21:37832200-37834000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr21:37832200-37836200	Weak transcription	HUVEC	blood vessel
26	chr21:37832600-37832800	Flanking Active TSS	Osteobl	bone
27	chr21:37832600-37833000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr21:37832600-37833400	Weak transcription	Fetal Lung	lung

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