Variant report

Variant	rs2049948
Chromosome Location	chr22:32808355-32808356
allele	A/G
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	chr22:32807960-32808434	K562	blood:	n/a	n/a
2	POLR2A	chr22:32807862-32808394	GM15510	blood:	n/a	n/a
3	RELA	chr22:32807450-32808564	GM19099	blood:	n/a	n/a
4	POLR2A	chr22:32807941-32808464	HEK293	kidney:	n/a	n/a
5	SIN3AK20	chr22:32807980-32808374	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr22:32807863-32808451	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr22:32807246-32808452	HepG2	liver:	n/a	n/a
8	HCFC1	chr22:32807542-32808919	Hela-S3	cervix:	n/a	n/a
9	REST	chr22:32808139-32808369	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr22:32807877-32808385	H1-neurons	neurons:	n/a	n/a
11	TCF7L2	chr22:32807577-32808532	PANC-1	pancreas:	n/a	chr22:32808175-32808189
12	POLR2A	chr22:32807866-32808377	GM12891	blood:	n/a	n/a
13	HA-E2F1	chr22:32807569-32808512	MCF-7	breast:	n/a	chr22:32808239-32808248
14	POLR2A	chr22:32807921-32808441	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr22:32807427-32808420	MCF10A-Er-Src	breast:	n/a	n/a
16	TBP	chr22:32807600-32808502	GM12878	blood:	n/a	n/a
17	GTF2F1	chr22:32807903-32808415	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr22:32807371-32808396	GM12891	blood:	n/a	n/a
19	POLR2A	chr22:32808054-32808357	K562	blood:	n/a	n/a
20	POLR2A	chr22:32807953-32808443	U87	brain:	n/a	n/a
21	SP1	chr22:32808047-32808392	GM12878	blood:	n/a	n/a
22	SMC3	chr22:32807688-32808375	Hela-S3	cervix:	n/a	chr22:32807840-32807848
23	EBF1	chr22:32808169-32808414	GM12878	blood:	n/a	n/a
24	TAF1	chr22:32808048-32808414	SK-N-SH	brain:	n/a	n/a
25	STAT1	chr22:32808104-32808355	GM12878	blood:	n/a	n/a
26	TBP	chr22:32808037-32808524	Hela-S3	cervix:	n/a	n/a
27	MYC	chr22:32808176-32808452	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF1	chr22:32807947-32808387	K562	blood:	n/a	n/a
29	TAF1	chr22:32807915-32808409	A549	lung:	n/a	n/a
30	NRF1	chr22:32808078-32808429	HepG2	liver:	n/a	chr22:32808238-32808249 chr22:32808238-32808249
31	E2F4	chr22:32808034-32808433	GM12878	blood:	n/a	chr22:32808239-32808248
32	TAF1	chr22:32807948-32808443	GM12878	blood:	n/a	n/a
33	POLR2A	chr22:32807791-32808361	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr22:32807768-32808574	HepG2	liver:	n/a	n/a
35	ZBTB33	chr22:32808095-32808394	A549	lung:	n/a	n/a
36	MXI1	chr22:32807404-32808455	GM12878	blood:	n/a	n/a
37	POLR2A	chr22:32807889-32808424	MCF-7	breast:	n/a	n/a
38	POLR2A	chr22:32807881-32808533	PBDE	blood:	n/a	n/a
39	YY1	chr22:32807911-32808424	GM12878	blood:	n/a	chr22:32808024-32808043 chr22:32808026-32808036 chr22:32807943-32807954
40	ZNF143	chr22:32807918-32808457	GM12878	blood:	n/a	n/a
41	POLR2A	chr22:32807912-32808400	PANC-1	pancreas:	n/a	n/a
42	FOS	chr22:32808141-32808361	MCF10A-Er-Src	breast:	n/a	n/a
43	HDAC2	chr22:32807793-32808455	HepG2	liver:	n/a	n/a
44	POLR2A	chr22:32807940-32808382	MCF-7	breast:	n/a	n/a
45	ZBTB33	chr22:32808067-32808412	A549	lung:	n/a	n/a
46	POLR2A	chr22:32807969-32808427	Raji	blood:	n/a	n/a
47	HEY1	chr22:32808030-32808370	K562	blood:	n/a	n/a
48	NRF1	chr22:32808067-32808429	K562	blood:	n/a	chr22:32808238-32808249 chr22:32808238-32808249
49	ELF1	chr22:32808120-32808390	HepG2	liver:	n/a	n/a
50	POLR2A	chr22:32807773-32808540	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:32806505..32810377-chr22:32871743..32874140,3	K562	blood:
2	chr22:32803479..32806391-chr22:32807402..32809274,3	MCF-7	breast:
3	chr22:32802183..32805062-chr22:32805761..32809013,3	MCF-7	breast:
4	chr22:32778843..32780459-chr22:32807463..32809458,2	K562	blood:
5	chr22:32807562..32810232-chr22:32869269..32871220,2	K562	blood:
6	chr22:32806622..32809672-chr22:32869373..32872144,4	MCF-7	breast:

Variant related genes	Relation type
RTCB	TF binding region
ENSG00000100220	Chromatin interaction
ENSG00000100225	Chromatin interaction
ENSG00000241954	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11913228	0.82[YRI][hapmap]
rs2076043	0.95[CHB][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5749430	0.95[CHB][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5754073	0.95[CHB][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs926308	0.95[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1055701	chr22:32806595-32845403	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2049948	TRIT1	trans	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32806400-32808600	Active TSS	Colonic Mucosa	Colon
2	chr22:32806400-32808600	Active TSS	Fetal Kidney	kidney
3	chr22:32806400-32808800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr22:32806600-32808400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr22:32806600-32808600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr22:32806600-32809000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr22:32806800-32808400	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr22:32806800-32808800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr22:32807000-32808400	Active TSS	H9 Cell Line	embryonic stem cell
10	chr22:32807000-32808400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr22:32807000-32808400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:32807000-32808600	Active TSS	Aorta	Aorta
13	chr22:32807000-32808800	Active TSS	Left Ventricle	heart
14	chr22:32807000-32808800	Active TSS	Psoas Muscle	Psoas
15	chr22:32807200-32808400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr22:32807200-32808400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr22:32807200-32808400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr22:32807200-32808400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr22:32807200-32808400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr22:32807200-32808400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr22:32807200-32808400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr22:32807200-32808400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr22:32807200-32808400	Active TSS	Placenta Amnion	Placenta Amnion
24	chr22:32807200-32808400	Active TSS	GM12878-XiMat	blood
25	chr22:32807200-32808400	Active TSS	HSMM	muscle
26	chr22:32807200-32808400	Active TSS	NH-A	brain
27	chr22:32807200-32808600	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr22:32807200-32808600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr22:32807200-32808600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr22:32807200-32808600	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr22:32807200-32808600	Active TSS	Fetal Intestine Large	intestine
32	chr22:32807200-32808600	Active TSS	Fetal Intestine Small	intestine
33	chr22:32807200-32808600	Active TSS	Fetal Muscle Trunk	muscle
34	chr22:32807200-32808600	Active TSS	Pancreas	Pancrea
35	chr22:32807200-32808600	Active TSS	A549	lung
36	chr22:32807200-32808600	Active TSS	K562	blood
37	chr22:32807200-32808800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr22:32807200-32808800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr22:32807200-32808800	Active TSS	Fetal Brain Female	brain
40	chr22:32807200-32808800	Active TSS	Fetal Stomach	stomach
41	chr22:32807200-32808800	Active TSS	Ovary	ovary
42	chr22:32807200-32808800	Active TSS	Right Atrium	heart
43	chr22:32807200-32808800	Active TSS	Right Ventricle	heart
44	chr22:32807200-32808800	Active TSS	NHDF-Ad	bronchial
45	chr22:32807400-32808400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr22:32807400-32808400	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr22:32807400-32808400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr22:32807400-32808400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr22:32807400-32808400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr22:32807400-32808400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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