Variant report

Variant	rs2242661
Chromosome Location	chr21:15755821-15755822
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	chr21:15754947-15756058	GM12891	blood:	n/a	n/a
2	SIN3A	chr21:15755302-15756038	GM12878	blood:	n/a	n/a
3	POLR2A	chr21:15755169-15756420	HL-60	blood:	n/a	n/a
4	CTBP2	chr21:15754868-15756205	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAZ	chr21:15754963-15756331	HepG2	liver:	n/a	chr21:15755046-15755056 chr21:15756219-15756228
6	MYC	chr21:15755431-15755873	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr21:15754962-15756979	Raji	blood:	n/a	n/a
8	PBX3	chr21:15755208-15755965	SK-N-SH	brain:	n/a	n/a
9	CREB1	chr21:15755139-15756003	HepG2	liver:	n/a	n/a
10	CREB1	chr21:15755093-15756036	K562	blood:	n/a	n/a
11	TAF1	chr21:15755683-15755968	PFSK-1	brain:	n/a	n/a
12	MAZ	chr21:15754760-15756387	K562	blood:	n/a	chr21:15755046-15755056 chr21:15756219-15756228
13	POLR2A	chr21:15755769-15755863	A549	lung:	n/a	n/a
14	PBX3	chr21:15755207-15756092	SK-N-SH	brain:	n/a	n/a
15	ELK1	chr21:15755079-15756214	GM12878	blood:	n/a	n/a
16	ELF1	chr21:15755298-15755937	MCF-7	breast:	n/a	n/a
17	ETS1	chr21:15755318-15756045	A549	lung:	n/a	chr21:15755487-15755498 chr21:15755525-15755538
18	ETS1	chr21:15755089-15756160	K562	blood:	n/a	chr21:15755487-15755498 chr21:15755525-15755538
19	ARID3A	chr21:15755268-15756109	HepG2	liver:	n/a	n/a
20	TEAD4	chr21:15755103-15756558	K562	blood:	n/a	n/a
21	WRNIP1	chr21:15754869-15756459	GM12878	blood:	n/a	n/a
22	JUND	chr21:15755262-15755863	HepG2	liver:	n/a	chr21:15755282-15755292 chr21:15755282-15755292
23	PML	chr21:15755111-15756371	K562	blood:	n/a	n/a
24	POLR2A	chr21:15755072-15756579	GM12878	blood:	n/a	n/a
25	POLR2A	chr21:15755004-15756465	GM15510	blood:	n/a	n/a
26	MAX	chr21:15755041-15755992	MCF-7	breast:	n/a	chr21:15755046-15755056
27	TBL1XR1	chr21:15754979-15756461	K562	blood:	n/a	n/a
28	BRCA1	chr21:15755348-15756047	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr21:15754784-15756487	H1-neurons	neurons:	n/a	n/a
30	GTF2F1	chr21:15754838-15756247	H1-hESC	embryonic stem cell:	n/a	n/a
31	ZBTB33	chr21:15755450-15755970	GM12878	blood:	n/a	chr21:15755741-15755756
32	ELF1	chr21:15755252-15755890	K562	blood:	n/a	n/a
33	POLR2A	chr21:15754958-15756130	GM12878	blood:	n/a	n/a
34	ZNF143	chr21:15754964-15756099	Hela-S3	cervix:	n/a	chr21:15755527-15755536 chr21:15755518-15755536 chr21:15755525-15755534 chr21:15755494-15755512
35	POLR2A	chr21:15754908-15756261	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr21:15755203-15756066	HepG2	liver:	n/a	n/a
37	POLR2A	chr21:15755729-15755950	HCT-116	colon:	n/a	n/a
38	BHLHE40	chr21:15755011-15756441	K562	blood:	n/a	chr21:15755215-15755231
39	POLR2A	chr21:15754822-15756627	H1-neurons	neurons:	n/a	n/a
40	CHD2	chr21:15755020-15756199	GM12878	blood:	n/a	n/a
41	GTF2F1	chr21:15755259-15756543	K562	blood:	n/a	n/a
42	REST	chr21:15754993-15756126	H1-neurons	neurons:	n/a	chr21:15756036-15756049
43	POLR2A	chr21:15754935-15756320	U87	brain:	n/a	n/a
44	POLR2A	chr21:15755614-15756178	K562	blood:	n/a	n/a
45	POLR2A	chr21:15754913-15756426	HEK293	kidney:	n/a	n/a
46	JUND	chr21:15755206-15755907	HepG2	liver:	n/a	chr21:15755282-15755292 chr21:15755282-15755292
47	PML	chr21:15755234-15756361	K562	blood:	n/a	n/a
48	POLR2A	chr21:15754754-15756759	Hela-S3	cervix:	n/a	n/a
49	YY1	chr21:15755248-15756557	GM12878	blood:	n/a	n/a
50	TAF1	chr21:15754965-15756257	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:15755528..15756150-chr5:33440838..33441550,2	Hela-S3	cervix:
2	chr12:56122664..56123207-chr21:15755194..15755994,2	Hela-S3	cervix:
3	chr21:15754870..15757296-chr21:16435942..16438083,2	K562	blood:
4	chr21:15645251..15647400-chr21:15754351..15756122,2	K562	blood:

Variant related genes	Relation type
HSPA13	TF binding region
ENSG00000180530	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000113407	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000243064	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1882881	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs2242662	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822646	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2822647	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2822648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822649	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2822650	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2822651	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2822661	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs28456168	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34396263	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35244754	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6516754	0.81[YRI][hapmap]
rs67163096	0.81[ASN][1000 genomes]
rs7281846	0.85[ASN][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	nsv1064554	chr21:15676222-15809321	Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1061686	chr21:15724570-15765777	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv913403	chr21:15743387-15786271	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2242661	HSPA13	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15753000-15756800	Active TSS	A549	lung
2	chr21:15753200-15756400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr21:15753200-15756600	Active TSS	Right Ventricle	heart
4	chr21:15753400-15756400	Active TSS	K562	blood
5	chr21:15753600-15756400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr21:15753600-15756800	Active TSS	Brain Germinal Matrix	brain
7	chr21:15753800-15756200	Active TSS	Brain Anterior Caudate	brain
8	chr21:15753800-15756400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr21:15753800-15756400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr21:15753800-15756600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr21:15753800-15756600	Active TSS	GM12878-XiMat	blood
12	chr21:15753800-15756600	Active TSS	NHLF	lung
13	chr21:15753800-15756800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr21:15753800-15756800	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr21:15754000-15756400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr21:15754000-15756400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr21:15754000-15756600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr21:15754000-15756800	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr21:15754200-15756400	Active TSS	Fetal Brain Female	brain
20	chr21:15754400-15756200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr21:15754400-15756200	Active TSS	Pancreas	Pancrea
22	chr21:15754400-15756200	Active TSS	HSMMtube	muscle
23	chr21:15754400-15756400	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr21:15754400-15756400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr21:15754400-15756400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr21:15754400-15756400	Active TSS	Colonic Mucosa	Colon
27	chr21:15754400-15756400	Active TSS	Ovary	ovary
28	chr21:15754400-15756600	Active TSS	H1 Cell Line	embryonic stem cell
29	chr21:15754400-15756600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr21:15754400-15756600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr21:15754400-15756600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr21:15754400-15756600	Active TSS	Psoas Muscle	Psoas
33	chr21:15754400-15756800	Active TSS	Right Atrium	heart
34	chr21:15754600-15756000	Active TSS	Stomach Mucosa	stomach
35	chr21:15754600-15756200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr21:15754600-15756200	Active TSS	Duodenum Mucosa	Duodenum
37	chr21:15754600-15756200	Active TSS	Fetal Muscle Leg	muscle
38	chr21:15754600-15756200	Active TSS	NHEK	skin
39	chr21:15754600-15756400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr21:15754600-15756400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr21:15754600-15756400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr21:15754600-15756400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr21:15754600-15756400	Active TSS	Aorta	Aorta
44	chr21:15754600-15756400	Active TSS	Brain Angular Gyrus	brain
45	chr21:15754600-15756400	Active TSS	Brain Hippocampus Middle	brain
46	chr21:15754600-15756400	Active TSS	Fetal Brain Male	brain
47	chr21:15754600-15756400	Active TSS	Fetal Intestine Small	intestine
48	chr21:15754600-15756400	Active TSS	Lung	lung
49	chr21:15754600-15756400	Active TSS	NHDF-Ad	bronchial
50	chr21:15754600-15756600	Active TSS	HUES6 Cell Line	embryonic stem cell

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