Variant report

Variant	rs1798177
Chromosome Location	chr11:57412150-57412151
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	chr11:57412029-57412725	U87	brain:	n/a	n/a
2	POLR2A	chr11:57412126-57412757	PANC-1	pancreas:	n/a	n/a
3	CTCF	chr11:57412143-57412636	HCT-116	colon:	n/a	chr11:57412446-57412464 chr11:57412441-57412462 chr11:57412448-57412461 chr11:57412447-57412463 chr11:57412452-57412461
4	MAZ	chr11:57411935-57413222	IMR90	lung:	n/a	n/a
5	POLR2A	chr11:57411937-57420676	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:57410796-57421100	H1-hESC	embryonic stem cell:	n/a	n/a
7	SMC3	chr11:57411987-57412843	SK-N-SH	brain:	n/a	chr11:57412448-57412462
8	POLR2A	chr11:57412052-57419760	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr11:57404829-57418710	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr11:57410821-57420904	H1-hESC	embryonic stem cell:	n/a	n/a
11	PML	chr11:57412147-57412713	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:57411938-57412844	ECC-1	luminal epithelium:	n/a	n/a
13	CTCF	chr11:57412040-57412190	GM12867	blood:	n/a	n/a
14	POLR2A	chr11:57411926-57416336	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr11:57412002-57412718	PANC-1	pancreas:	n/a	n/a
16	CTCF	chr11:57412075-57412798	HCT-116	colon:	n/a	chr11:57412446-57412464 chr11:57412441-57412462 chr11:57412448-57412461 chr11:57412447-57412463 chr11:57412452-57412461
17	POLR2A	chr11:57411980-57417263	H1-hESC	embryonic stem cell:	n/a	n/a
18	SP4	chr11:57412135-57412675	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr11:57412035-57412693	U87	brain:	n/a	n/a
20	POLR2A	chr11:57411982-57412860	H1-hESC	embryonic stem cell:	n/a	n/a
21	RAD21	chr11:57412089-57412787	HCT-116	colon:	n/a	chr11:57412447-57412460 chr11:57412444-57412463
22	RAD21	chr11:57412051-57412730	H1-hESC	embryonic stem cell:	n/a	chr11:57412447-57412460 chr11:57412444-57412463
23	CTCF	chr11:57411952-57413217	SK-N-SH	brain:	n/a	chr11:57412446-57412464 chr11:57412441-57412462 chr11:57412448-57412461 chr11:57412447-57412463 chr11:57412452-57412461
24	RAD21	chr11:57412121-57412592	MCF-7	breast:	n/a	chr11:57412447-57412460 chr11:57412444-57412463
25	RAD21	chr11:57412034-57412806	HCT-116	colon:	n/a	chr11:57412447-57412460 chr11:57412444-57412463
26	POLR2A	chr11:57404802-57417187	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr11:57412040-57416702	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr11:57411922-57418069	SK-N-SH	brain:	n/a	n/a
29	RAD21	chr11:57412109-57412707	A549	lung:	n/a	chr11:57412447-57412460 chr11:57412444-57412463
30	POLR2A	chr11:57411868-57413914	HepG2	liver:	n/a	n/a
31	CTCF	chr11:57412034-57413126	A549	lung:	n/a	chr11:57412446-57412464 chr11:57412441-57412462 chr11:57412448-57412461 chr11:57412447-57412463 chr11:57412452-57412461
32	POLR2A	chr11:57410100-57417938	PBDE	blood:	n/a	n/a
33	ATF2	chr11:57412150-57413233	H1-hESC	embryonic stem cell:	n/a	n/a
34	ZNF143	chr11:57412129-57412635	H1-hESC	embryonic stem cell:	n/a	n/a
35	RAD21	chr11:57411926-57412837	SK-N-SH	brain:	n/a	chr11:57412447-57412460 chr11:57412444-57412463
36	POLR2A	chr11:57409804-57420281	PFSK-1	brain:	n/a	n/a
37	ATF2	chr11:57412065-57412666	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr11:57412031-57412783	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr11:57412045-57412804	HepG2	liver:	n/a	n/a
40	RAD21	chr11:57412150-57412626	A549	lung:	n/a	chr11:57412447-57412460 chr11:57412444-57412463

No.	Distal block	Cell Line	Cell type
1	chr11:57411538..57413091-chr11:57423300..57425446,2	K562	blood:
2	chr11:57334311..57335222-chr11:57412048..57412889,2	K562	blood:
3	chr11:57334278..57336865-chr11:57411196..57413730,2	K562	blood:
4	chr11:57260580..57261537-chr11:57411949..57412991,4	K562	blood:
5	chr11:57224560..57225436-chr11:57411980..57412884,2	K562	blood:
6	chr11:57411538..57415148-chr11:57422707..57424942,3	K562	blood:
7	chr11:57335286..57336293-chr11:57411795..57412862,4	K562	blood:
8	chr11:57335629..57336368-chr11:57411973..57412866,2	MCF-7	breast:
9	chr11:57225611..57226757-chr11:57411990..57412532,3	K562	blood:
10	chr11:57258888..57259762-chr11:57412016..57412949,3	MCF-7	breast:
11	chr11:57113255..57113767-chr11:57411943..57412895,2	K562	blood:

Variant related genes	Relation type
ENSG00000254602	TF binding region
CLP1	TF binding region
ENSG00000156587	Chromatin interaction
ENSG00000172409	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10792110	1.00[JPT][hapmap]
rs10896644	1.00[JPT][hapmap]
rs10896649	1.00[JPT][hapmap]
rs11229109	1.00[JPT][hapmap]
rs11570176	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11570181	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1613592	0.84[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1631684	0.81[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1647394	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1647403	0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17455422	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1783826	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1783827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783828	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783829	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1783978	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1783979	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1783980	1.00[JPT][hapmap]
rs1783981	1.00[JPT][hapmap]
rs1783983	0.84[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1783984	0.85[AMR][1000 genomes]
rs1783985	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1785498	1.00[JPT][hapmap]
rs1798172	0.84[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1798173	0.81[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2156638	1.00[JPT][hapmap]
rs2956981	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs3017889	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs36036499	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4611222	1.00[JPT][hapmap]
rs627145	1.00[JPT][hapmap]
rs653889	1.00[JPT][hapmap]
rs665058	1.00[JPT][hapmap]
rs7117020	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7120868	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7947357	1.00[CEU][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs929934	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	esv992553	chr11:57408294-57419351	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1798177	VWCE	cis	cerebellum	SCAN
rs1798177	TIMM10	cis	Esophagus Mucosa	GTEx
rs1798177	OR5B17	cis	parietal	SCAN
rs1798177	MS4A7	cis	parietal	SCAN
rs1798177	CD5	cis	parietal	SCAN
rs1798177	YPEL4	cis	lymphoblastoid	seeQTL
rs1798177	YPEL4	cis	lung	GTEx
rs1798177	TNKS1BP1	cis	parietal	SCAN
rs1798177	SLC43A3	cis	cerebellum	SCAN
rs1798177	TIMM10	cis	parietal	SCAN
rs1798177	TIMM10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57403000-57412200	Weak transcription	Hela-S3	cervix
2	chr11:57407200-57412200	Weak transcription	Ovary	ovary
3	chr11:57407400-57412600	Weak transcription	GM12878-XiMat	blood
4	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr11:57407600-57412200	Weak transcription	Spleen	Spleen
7	chr11:57407600-57413000	Weak transcription	Right Ventricle	heart
8	chr11:57407600-57413200	Weak transcription	Esophagus	oesophagus
9	chr11:57407800-57412200	Weak transcription	Pancreas	Pancrea
10	chr11:57408000-57412200	Weak transcription	Lung	lung
11	chr11:57408400-57412200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:57408800-57412200	Weak transcription	Adipose Nuclei	Adipose
13	chr11:57408800-57412200	Weak transcription	Brain Hippocampus Middle	brain
14	chr11:57408800-57412200	Weak transcription	Thymus	Thymus
15	chr11:57408800-57412600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:57408800-57412600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:57408800-57413400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr11:57409000-57412200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:57409000-57412200	Weak transcription	Brain Substantia Nigra	brain
20	chr11:57409000-57412200	Weak transcription	Fetal Intestine Small	intestine
21	chr11:57409000-57412200	Weak transcription	Fetal Kidney	kidney
22	chr11:57409000-57412200	Weak transcription	A549	lung
23	chr11:57409000-57412200	Weak transcription	HSMMtube	muscle
24	chr11:57409000-57413200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:57409000-57414400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:57409000-57416200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr11:57409200-57412200	Weak transcription	Liver	Liver
28	chr11:57409200-57412200	Weak transcription	HepG2	liver
29	chr11:57409200-57412200	Weak transcription	Osteobl	bone
30	chr11:57409200-57413600	Weak transcription	Primary T cells from cord blood	blood
31	chr11:57409400-57413000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:57409600-57412200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:57409600-57412200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:57409600-57412200	Weak transcription	NH-A	brain
35	chr11:57409600-57412200	Weak transcription	NHDF-Ad	bronchial
36	chr11:57409600-57412800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:57409600-57413200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:57409600-57413200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:57409600-57413200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr11:57409600-57413600	Weak transcription	HMEC	breast
41	chr11:57409600-57414000	Weak transcription	Brain Germinal Matrix	brain
42	chr11:57410000-57414200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr11:57410200-57413400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:57410400-57412200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr11:57410400-57412200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr11:57410400-57412600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:57410600-57412600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr11:57411000-57412200	Enhancers	HUVEC	blood vessel
49	chr11:57411000-57413400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:57411000-57414600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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