Variant report

Variant	rs2838675
Chromosome Location	chr21:46182376-46182377
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	chr21:46180771..46183502-chr21:46265966..46267491,2	MCF-7	breast:
2	chr21:46168780..46172261-chr21:46182031..46184514,3	K562	blood:
3	chr21:46181841..46189587-chr21:46189919..46197097,16	MCF-7	breast:
4	chr21:46171917..46177806-chr21:46181342..46188371,13	MCF-7	breast:
5	chr21:46182055..46185052-chr21:46201680..46204266,2	MCF-7	breast:
6	chr21:46181402..46184380-chr21:46359332..46361437,2	K562	blood:
7	chr21:46175791..46179741-chr21:46180006..46182976,4	K562	blood:
8	chr21:46181840..46185418-chr21:46198665..46202269,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184787	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000160256	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1071792	0.81[EUR][1000 genomes]
rs1109280	0.84[CEU][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs11702064	0.85[CHD][hapmap]
rs1347324	0.84[EUR][1000 genomes]
rs1821431	0.85[EUR][1000 genomes]
rs2294157	0.85[EUR][1000 genomes]
rs2329899	0.84[EUR][1000 genomes]
rs2329900	0.84[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs2838673	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838674	1.00[ASN][1000 genomes]
rs2838678	0.85[EUR][1000 genomes]
rs2838686	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2838699	0.92[CHD][hapmap]
rs3788136	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs4239838	0.84[CEU][hapmap];0.85[CHD][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs4818973	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818974	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818975	0.84[CEU][hapmap];0.85[CHD][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs55659309	1.00[ASN][1000 genomes]
rs62222752	0.80[EUR][1000 genomes]
rs6518204	0.85[CHD][hapmap]
rs733161	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760430	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs760431	0.84[CEU][hapmap];0.85[CHD][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs8103	0.84[CEU][hapmap];0.92[CHD][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs8128992	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8133039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs885655	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2838675	PTTG1IP	cis	parietal	SCAN
rs2838675	NCRNA00175	cis	parietal	SCAN
rs2838675	C21orf58	cis	parietal	SCAN
rs2838675	UBE2G2	Cis_1M	lymphoblastoid	RTeQTL
rs2838675	RIPK4	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46168000-46185800	Weak transcription	Right Atrium	heart
2	chr21:46171400-46183400	Weak transcription	Gastric	stomach
3	chr21:46179000-46183400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr21:46179600-46184600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr21:46180400-46182600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr21:46180800-46183400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:46180800-46184800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr21:46181200-46188000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr21:46181400-46183000	Flanking Active TSS	HepG2	liver
10	chr21:46181600-46182400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr21:46181600-46184800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr21:46181600-46185000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr21:46181800-46182600	Enhancers	Liver	Liver
14	chr21:46181800-46183000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr21:46181800-46184400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr21:46181800-46184400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr21:46181800-46185000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr21:46181800-46185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr21:46181800-46188000	Weak transcription	Fetal Intestine Small	intestine
20	chr21:46181800-46188400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr21:46182000-46183800	Weak transcription	Esophagus	oesophagus
22	chr21:46182000-46184600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr21:46182000-46184600	Weak transcription	K562	blood
24	chr21:46182000-46186400	Weak transcription	Fetal Muscle Leg	muscle
25	chr21:46182200-46183200	Weak transcription	HMEC	breast
26	chr21:46182200-46185000	Weak transcription	Fetal Intestine Large	intestine
27	chr21:46182200-46189000	Weak transcription	Rectal Mucosa Donor 31	rectum

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