Variant report

Variant	rs2094874
Chromosome Location	chr21:40753007-40753008
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	chr21:40751803-40753200	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr21:40752900-40753145	HCT-116	colon:	n/a	n/a
3	POLR2A	chr21:40752989-40753024	MCF-7	breast:	n/a	n/a
4	POLR2A	chr21:40752914-40753180	HCT-116	colon:	n/a	n/a
5	HDAC2	chr21:40751825-40753383	MCF-7	breast:	n/a	chr21:40752025-40752039 chr21:40752024-40752038 chr21:40752021-40752035 chr21:40752020-40752034
6	POLR2A	chr21:40751933-40753492	IMR90	lung:	n/a	n/a
7	POLR2A	chr21:40752883-40753202	Hela-S3	cervix:	n/a	n/a
8	RFX5	chr21:40752984-40753242	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr21:40752980-40753130	HUVEC	blood vessel:	n/a	chr21:40753071-40753078
10	POLR2A	chr21:40752785-40753214	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr21:40752049-40753085	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr21:40751707-40753530	SK-N-SH	brain:	n/a	n/a
13	SIN3A	chr21:40752078-40753090	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAZ	chr21:40752963-40753252	Hela-S3	cervix:	n/a	n/a
15	ZNF263	chr21:40752921-40753312	HEK293-T-REx	kidney:	n/a	n/a
16	HA-E2F1	chr21:40752867-40753474	MCF-7	breast:	n/a	n/a
17	TBP	chr21:40752924-40753191	Hela-S3	cervix:	n/a	n/a
18	E2F6	chr21:40751949-40753146	K562	blood:	n/a	chr21:40752232-40752241 chr21:40752160-40752169
19	RCOR1	chr21:40751981-40753200	K562	blood:	n/a	n/a
20	RCOR1	chr21:40752015-40753279	Hela-S3	cervix:	n/a	n/a
21	SIN3AK20	chr21:40751737-40753595	MCF-7	breast:	n/a	n/a
22	POLR2A	chr21:40752864-40753200	ProgFib	skin:	n/a	n/a
23	POLR2A	chr21:40752827-40753150	U87	brain:	n/a	n/a
24	POLR2A	chr21:40752820-40753228	U87	brain:	n/a	n/a
25	POLR2A	chr21:40752009-40753503	K562	blood:	n/a	n/a
26	POLR2A	chr21:40751800-40753180	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr21:40753000-40753150	Hela-S3	cervix:	n/a	chr21:40753071-40753078
28	POLR2A	chr21:40752912-40753260	K562	blood:	n/a	n/a
29	POLR2A	chr21:40752843-40753264	MCF-7	breast:	n/a	n/a
30	MAX	chr21:40751929-40753434	MCF-7	breast:	n/a	n/a
31	SMC3	chr21:40752909-40753247	Hela-S3	cervix:	n/a	n/a
32	HCFC1	chr21:40751518-40753804	Hela-S3	cervix:	n/a	n/a
33	MXI1	chr21:40751890-40753180	IMR90	lung:	n/a	n/a
34	CTCF	chr21:40753000-40753150	MCF-7	breast:	n/a	chr21:40753071-40753078
35	POLR2A	chr21:40751945-40753125	H1-neurons	neurons:	n/a	n/a
36	REST	chr21:40751817-40753508	H1-neurons	neurons:	n/a	chr21:40752290-40752303 chr21:40752258-40752276 chr21:40752653-40752666 chr21:40752978-40752991 chr21:40752283-40752296 chr21:40752789-40752809 chr21:40753183-40753192
37	POLR2A	chr21:40752035-40753118	H1-neurons	neurons:	n/a	n/a
38	MAZ	chr21:40751979-40753420	IMR90	lung:	n/a	n/a
39	POLR2A	chr21:40751931-40753270	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40683876..40687631-chr21:40749667..40753921,6	K562	blood:
2	chr21:40716961..40718462-chr21:40751682..40753726,2	K562	blood:
3	chr21:40750891..40755008-chr21:40755976..40761346,13	MCF-7	breast:
4	chr21:40691963..40695047-chr21:40751458..40754017,3	MCF-7	breast:
5	chr21:40683489..40689074-chr21:40750757..40754639,9	MCF-7	breast:
6	chr21:40752170..40754899-chr21:40764074..40766605,2	MCF-7	breast:
7	chr21:40719359..40724848-chr21:40748806..40754741,7	MCF-7	breast:
8	chr21:40553583..40556349-chr21:40752514..40754766,2	K562	blood:
9	chr21:40716662..40723444-chr21:40748337..40754328,16	MCF-7	breast:
10	chr21:40716961..40722807-chr21:40750720..40754894,10	K562	blood:
11	chr21:40685228..40687774-chr21:40751832..40753804,3	K562	blood:
12	chr21:40750392..40754801-chr21:40757428..40762186,12	MCF-7	breast:
13	chr21:40719750..40724652-chr21:40748317..40754270,9	K562	blood:
14	chr21:40750855..40754449-chr21:40757264..40761324,13	K562	blood:
15	chr21:40683271..40692626-chr21:40743960..40754349,22	MCF-7	breast:
16	chr21:40750443..40753981-chr21:40814998..40818130,3	MCF-7	breast:
17	chr21:40750751..40754678-chr21:40755594..40761324,12	K562	blood:

Variant related genes	Relation type
RNF6P1	TF binding region
ENSG00000238141	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000238556	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000185437	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1060180	0.83[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10775662	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11701047	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13049783	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13051571	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13051949	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13230	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2299739	0.90[EUR][1000 genomes]
rs2299741	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836994	0.83[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836995	0.92[CHB][hapmap]
rs2836996	0.93[CHB][hapmap]
rs2836997	0.94[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836998	0.83[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2836999	0.88[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2837000	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2837001	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2837002	0.82[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2837003	0.85[CHB][hapmap]
rs2837004	0.85[CHB][hapmap]
rs2837005	0.88[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2837006	0.88[CEU][hapmap];0.85[CHB][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2837007	0.88[CEU][hapmap];0.85[CHB][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2837008	0.82[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3787923	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3787924	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4816624	0.86[JPT][hapmap]
rs4818031	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4818032	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4818033	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4818035	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4818036	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6517547	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8131718	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9305674	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9974828	0.88[CEU][hapmap];0.84[CHB][hapmap];0.90[EUR][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	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	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
3	nsv1056452	chr21:40741893-40782587	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1063521	chr21:40747754-40790197	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2094874	SH3BGR	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40751600-40753400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr21:40751600-40753400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr21:40751600-40753400	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr21:40751600-40753400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr21:40751600-40753600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr21:40751800-40753200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:40751800-40753200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr21:40751800-40753400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr21:40751800-40753400	Active TSS	Aorta	Aorta
10	chr21:40751800-40753400	Active TSS	Fetal Intestine Large	intestine
11	chr21:40751800-40753400	Active TSS	Right Atrium	heart
12	chr21:40751800-40753400	Active TSS	NHDF-Ad	bronchial
13	chr21:40751800-40753600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr21:40751800-40753600	Active TSS	H1 Cell Line	embryonic stem cell
15	chr21:40751800-40753600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr21:40751800-40753600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr21:40751800-40753600	Active TSS	A549	lung
18	chr21:40752000-40753200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr21:40752000-40753200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr21:40752000-40753200	Active TSS	Esophagus	oesophagus
21	chr21:40752000-40753200	Active TSS	Ovary	ovary
22	chr21:40752000-40753400	Active TSS	H9 Cell Line	embryonic stem cell
23	chr21:40752000-40753400	Active TSS	HSMM	muscle
24	chr21:40752000-40753600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr21:40752200-40753400	Active TSS	Muscle Satellite Cultured Cells	--
26	chr21:40752200-40753400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr21:40752200-40753600	Active TSS	NHLF	lung
28	chr21:40752400-40753200	Flanking Active TSS	Liver	Liver
29	chr21:40752400-40753200	Flanking Active TSS	Placenta	Placenta
30	chr21:40752400-40753200	Bivalent/Poised TSS	HepG2	liver
31	chr21:40752400-40753400	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr21:40752400-40753400	Flanking Active TSS	Colonic Mucosa	Colon
33	chr21:40752600-40753200	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr21:40752600-40753200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr21:40752600-40753200	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr21:40752600-40753400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr21:40752600-40753600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr21:40752600-40753600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr21:40752800-40753200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr21:40752800-40753200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr21:40752800-40753200	Flanking Active TSS	Fetal Lung	lung
42	chr21:40752800-40753200	Flanking Active TSS	Fetal Thymus	thymus
43	chr21:40752800-40753200	Flanking Active TSS	Lung	lung
44	chr21:40752800-40753200	Flanking Active TSS	Thymus	Thymus
45	chr21:40752800-40753200	Flanking Active TSS	Spleen	Spleen
46	chr21:40752800-40753400	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr21:40752800-40753400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr21:40752800-40753400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr21:40752800-40753400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr21:40752800-40753400	Flanking Active TSS	Duodenum Mucosa	Duodenum

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