Variant report

Variant	rs17241025
Chromosome Location	chr21:16332923-16332924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:16329957-16333463	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr21:16332822-16333408	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr21:16329354-16336336	HepG2	liver:	n/a	n/a
4	POLR2A	chr21:16330516-16334228	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:16331957..16335486-chr21:16435819..16438054,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229047	TF binding region
ENSG00000180530	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10482863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12481775	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2228508	0.90[YRI][hapmap]
rs2822998	0.81[ASW][hapmap]
rs35324633	0.83[AFR][1000 genomes]
rs3787576	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6517118	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060151	chr21:16295713-16435497	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv544378	chr21:16295713-16435497	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv834048	chr21:16324481-16489570	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17241025	MIR623	trans	lymphoblastoid	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16313200-16334800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr21:16315600-16338000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr21:16322400-16339200	Weak transcription	Pancreas	Pancrea
4	chr21:16328000-16335800	Weak transcription	Dnd41	blood
5	chr21:16328200-16334400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr21:16328200-16335600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr21:16328200-16335600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr21:16328200-16338800	Weak transcription	HUVEC	blood vessel
9	chr21:16328400-16334400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:16328600-16335600	Weak transcription	K562	blood
11	chr21:16328600-16337600	Weak transcription	Psoas Muscle	Psoas
12	chr21:16328800-16335800	Weak transcription	Fetal Muscle Leg	muscle
13	chr21:16328800-16337200	Weak transcription	Left Ventricle	heart
14	chr21:16328800-16339400	Weak transcription	Ovary	ovary
15	chr21:16328800-16341600	Weak transcription	Hela-S3	cervix
16	chr21:16329000-16338000	Weak transcription	Placenta	Placenta
17	chr21:16329600-16335600	Weak transcription	Fetal Kidney	kidney
18	chr21:16329600-16338400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr21:16329600-16338800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr21:16330000-16335400	Weak transcription	HSMM	muscle
21	chr21:16330000-16337600	Weak transcription	Fetal Stomach	stomach
22	chr21:16330200-16335400	Weak transcription	HMEC	breast
23	chr21:16330400-16334800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr21:16330400-16335400	Weak transcription	NH-A	brain
25	chr21:16330400-16338600	Weak transcription	NHLF	lung
26	chr21:16330600-16337200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr21:16330800-16334600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr21:16330800-16335400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr21:16331000-16335600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr21:16331000-16335800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr21:16331000-16337400	Weak transcription	Osteobl	bone
32	chr21:16331000-16337800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr21:16331000-16338600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr21:16331000-16338600	Weak transcription	Brain Hippocampus Middle	brain
35	chr21:16331000-16338800	Weak transcription	Colon Smooth Muscle	Colon
36	chr21:16331400-16335600	Weak transcription	HepG2	liver
37	chr21:16331400-16339200	Weak transcription	Brain Substantia Nigra	brain
38	chr21:16331400-16339600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr21:16331600-16334600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr21:16331600-16335800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr21:16331600-16338000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr21:16331600-16341800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr21:16331800-16340200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr21:16332000-16337600	Weak transcription	Liver	Liver
45	chr21:16332200-16334800	Weak transcription	Primary B cells from cord blood	blood
46	chr21:16332200-16335400	Weak transcription	A549	lung
47	chr21:16332200-16338000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr21:16332400-16334600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr21:16332800-16337200	Weak transcription	Primary monocytes fromperipheralblood	blood

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