Variant report

Variant	rs1872126
Chromosome Location	chr11:72395535-72395536
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	USF1	chr11:72395250-72395537	K562	blood:	n/a	n/a
2	CTCF	chr11:72395484-72396030	MCF-7	breast:	n/a	chr11:72395750-72395759 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
3	CTCF	chr11:72395521-72395900	K562	blood:	n/a	chr11:72395750-72395759 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
4	RAD21	chr11:72395467-72396040	A549	lung:	n/a	chr11:72395633-72395643 chr11:72395751-72395764 chr11:72395803-72395816 chr11:72395753-72395763 chr11:72395632-72395645
5	CTCF	chr11:72394522-72396150	HCT-116	colon:	n/a	chr11:72395750-72395759 chr11:72395020-72395030 chr11:72394724-72394732 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72394952-72394970 chr11:72394954-72394967 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
6	RAD21	chr11:72394555-72396153	SK-N-SH	brain:	n/a	chr11:72395633-72395643 chr11:72394701-72394711 chr11:72394950-72394969 chr11:72395751-72395764 chr11:72395021-72395031 chr11:72395803-72395816 chr11:72394701-72394713 chr11:72395753-72395763 chr11:72395632-72395645
7	EBF1	chr11:72395411-72395763	GM12878	blood:	n/a	chr11:72395528-72395541 chr11:72395529-72395539 chr11:72395530-72395539 chr11:72395530-72395539
8	CTCF	chr11:72394726-72396031	HCT-116	colon:	n/a	chr11:72395750-72395759 chr11:72395020-72395030 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72394952-72394970 chr11:72394954-72394967 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
9	USF1	chr11:72395231-72395649	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr11:72395400-72395550	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr11:72388985-72396153	GM12892	blood:	n/a	n/a
12	NR2F2	chr11:72395407-72396061	K562	blood:	n/a	n/a
13	POLR2A	chr11:72393504-72395948	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:72391380-72396040	HL-60	blood:	n/a	n/a
15	POLR2A	chr11:72388899-72396049	K562	blood:	n/a	n/a
16	RAD21	chr11:72395513-72395929	MCF-7	breast:	n/a	chr11:72395633-72395643 chr11:72395751-72395764 chr11:72395803-72395816 chr11:72395753-72395763 chr11:72395632-72395645
17	FOSL1	chr11:72395535-72396000	K562	blood:	n/a	chr11:72395781-72395789 chr11:72395780-72395790
18	POLR2A	chr11:72389086-72395911	GM12892	blood:	n/a	n/a
19	POLR2A	chr11:72388792-72395937	GM12891	blood:	n/a	n/a
20	POLR2A	chr11:72388800-72396117	GM12878	blood:	n/a	n/a
21	RAD21	chr11:72395519-72396023	ECC-1	luminal epithelium:	n/a	chr11:72395633-72395643 chr11:72395751-72395764 chr11:72395803-72395816 chr11:72395753-72395763 chr11:72395632-72395645
22	RAD21	chr11:72395462-72395880	MCF-7	breast:	n/a	chr11:72395633-72395643 chr11:72395751-72395764 chr11:72395803-72395816 chr11:72395753-72395763 chr11:72395632-72395645
23	HMGN3	chr11:72395513-72396040	K562	blood:	n/a	n/a
24	FOSL2	chr11:72395480-72395994	A549	lung:	n/a	chr11:72395781-72395789 chr11:72395780-72395790
25	POLR2A	chr11:72394517-72396053	GM12878	blood:	n/a	n/a
26	USF1	chr11:72395197-72395668	ECC-1	luminal epithelium:	n/a	n/a
27	CTCF	chr11:72394603-72396062	MCF-7	breast:	n/a	chr11:72395750-72395759 chr11:72395020-72395030 chr11:72394724-72394732 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72394952-72394970 chr11:72394954-72394967 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
28	POLR2A	chr11:72389164-72395995	GM12878	blood:	n/a	n/a
29	CTCF	chr11:72395514-72395897	GM12878	blood:	n/a	chr11:72395750-72395759 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
30	CTCF	chr11:72394276-72396282	A549	lung:	n/a	chr11:72395750-72395759 chr11:72395020-72395030 chr11:72394724-72394732 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72394952-72394970 chr11:72394954-72394967 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
31	USF1	chr11:72395236-72395592	H1-hESC	embryonic stem cell:	n/a	n/a
32	EBF1	chr11:72395410-72395621	GM12878	blood:	n/a	chr11:72395528-72395541 chr11:72395529-72395539 chr11:72395530-72395539 chr11:72395530-72395539
33	HCFC1	chr11:72394439-72396120	Hela-S3	cervix:	n/a	n/a
34	RAD21	chr11:72395514-72395992	H1-hESC	embryonic stem cell:	n/a	chr11:72395633-72395643 chr11:72395751-72395764 chr11:72395803-72395816 chr11:72395753-72395763 chr11:72395632-72395645
35	RAD21	chr11:72395514-72395966	A549	lung:	n/a	chr11:72395633-72395643 chr11:72395751-72395764 chr11:72395803-72395816 chr11:72395753-72395763 chr11:72395632-72395645
36	SMC3	chr11:72395388-72396122	SK-N-SH	brain:	n/a	chr11:72395749-72395763 chr11:72395633-72395647
37	CTCF	chr11:72394592-72395939	GM12892	blood:	n/a	chr11:72395750-72395759 chr11:72395020-72395030 chr11:72394724-72394732 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72394952-72394970 chr11:72394954-72394967 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
38	POLR2A	chr11:72395246-72395910	K562	blood:	n/a	n/a
39	CTCF	chr11:72395520-72396058	K562	blood:	n/a	chr11:72395750-72395759 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
40	JUND	chr11:72395526-72395949	A549	lung:	n/a	chr11:72395781-72395789 chr11:72395779-72395790 chr11:72395780-72395790
41	CTCF	chr11:72394465-72396187	SK-N-SH	brain:	n/a	chr11:72395750-72395759 chr11:72395020-72395030 chr11:72394724-72394732 chr11:72395747-72395765 chr11:72395637-72395646 chr11:72395633-72395646 chr11:72394952-72394970 chr11:72394954-72394967 chr11:72395634-72395644 chr11:72395750-72395763 chr11:72395804-72395817
42	USF2	chr11:72395270-72395930	Hela-S3	cervix:	n/a	chr11:72395385-72395396

No.	Distal block	Cell Line	Cell type
1	chr11:72300650..72301426-chr11:72395181..72396064,3	MCF-7	breast:
2	chr11:72386808..72388323-chr11:72393446..72395639,2	K562	blood:
3	chr11:72309161..72310639-chr11:72394269..72395813,13	MCF-7	breast:
4	chr11:72296452..72297372-chr11:72394539..72395851,6	K562	blood:
5	chr11:72353865..72354782-chr11:72394923..72395729,2	MCF-7	breast:
6	chr11:71933813..71936010-chr11:72394188..72397078,2	MCF-7	breast:
7	chr11:72395003..72395663-chr11:72523411..72524058,2	MCF-7	breast:
8	chr11:72300511..72301381-chr11:72394523..72395807,4	MCF-7	breast:
9	chr11:72392980..72396012-chr11:72397929..72401582,3	K562	blood:
10	chr11:72395278..72395853-chr11:72559578..72560571,3	K562	blood:
11	chr11:72390674..72393188-chr11:72394273..72396002,3	MCF-7	breast:
12	chr11:72394933..72395858-chr11:72953383..72954110,3	K562	blood:
13	chr11:72296372..72297374-chr11:72394518..72396001,14	MCF-7	breast:
14	chr11:72310603..72311371-chr11:72394905..72395850,2	MCF-7	breast:

Variant related genes	Relation type
ARAP1-AS1	TF binding region
ENSG00000165458	Chromatin interaction
ENSG00000186642	Chromatin interaction
ENSG00000186635	Chromatin interaction
ENSG00000255808	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10793036	0.81[CHB][hapmap]
rs10898866	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs11235557	0.84[ASN][1000 genomes]
rs11235558	0.84[ASN][1000 genomes]
rs11235559	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs11235569	0.85[CEU][hapmap]
rs11235575	0.92[CEU][hapmap]
rs11607038	0.84[JPT][hapmap]
rs12146545	1.00[CHB][hapmap]
rs12362256	0.83[ASN][1000 genomes]
rs12363065	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs12576046	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12576058	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12786302	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12787293	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12797368	0.84[ASN][1000 genomes]
rs12797791	0.93[CHB][hapmap]
rs12799451	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12802369	0.97[ASN][1000 genomes]
rs12804316	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1391888	1.00[CHB][hapmap]
rs163694	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs168175	0.81[ASN][1000 genomes]
rs189332	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1980089	0.81[CHB][hapmap]
rs2035467	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2037030	0.84[ASN][1000 genomes]
rs2291289	0.85[CEU][hapmap]
rs2306607	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs2306609	0.87[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2306616	0.84[JPT][hapmap]
rs341052	0.93[CHB][hapmap]
rs341053	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs341060	0.87[ASN][1000 genomes]
rs341061	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs341062	0.85[ASN][1000 genomes]
rs34142547	0.98[ASN][1000 genomes]
rs342322	0.84[ASN][1000 genomes]
rs34285624	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34802028	0.98[ASN][1000 genomes]
rs35748558	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758934	0.90[ASN][1000 genomes]
rs3758935	0.92[ASN][1000 genomes]
rs3758936	0.92[ASN][1000 genomes]
rs3781913	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3781916	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs458275	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs458575	0.81[CHB][hapmap]
rs7125221	0.88[CEU][hapmap]
rs7126790	0.91[ASN][1000 genomes]
rs900613	0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs900614	0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs900615	0.89[ASN][1000 genomes]
rs90409	0.86[CHB][hapmap]

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	esv1806140	chr11:72268466-72546175	Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	77 gene(s)	inside rSNPs	diseases
2	nsv832207	chr11:72272750-72469122	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
3	nsv523601	chr11:72281884-72430935	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
4	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1872126	ARAP1	cis	cerebellum	SCAN
rs1872126	NADSYN1	cis	cerebellum	SCAN
rs1872126	UVRAG	cis	parietal	SCAN
rs1872126	KRTAP5-10	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72388000-72397200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr11:72388200-72396400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr11:72388600-72396000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:72389600-72397800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr11:72390000-72397000	Weak transcription	Primary B cells from cord blood	blood
6	chr11:72390200-72397800	Weak transcription	HepG2	liver
7	chr11:72391200-72396400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr11:72391400-72395800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:72391400-72403800	Weak transcription	Small Intestine	intestine
10	chr11:72391800-72398600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr11:72392200-72402600	Weak transcription	HUVEC	blood vessel
12	chr11:72392600-72395600	Weak transcription	Ovary	ovary
13	chr11:72392800-72395600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:72392800-72395800	Weak transcription	Fetal Heart	heart
15	chr11:72392800-72396200	Weak transcription	Pancreas	Pancrea
16	chr11:72392800-72396800	Weak transcription	Fetal Brain Male	brain
17	chr11:72392800-72397200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:72392800-72397400	Weak transcription	Brain Anterior Caudate	brain
19	chr11:72392800-72404000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:72392800-72404800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:72392800-72405600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:72393000-72397200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:72393000-72398200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:72393200-72395800	Weak transcription	NHEK	skin
25	chr11:72393200-72398400	Weak transcription	Aorta	Aorta
26	chr11:72393200-72400800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr11:72393200-72403800	Weak transcription	Fetal Kidney	kidney
28	chr11:72393400-72396200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:72393800-72395800	Strong transcription	Fetal Stomach	stomach
30	chr11:72393800-72413400	Strong transcription	Fetal Intestine Small	intestine
31	chr11:72393800-72423200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr11:72394000-72398200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:72394000-72399600	Genic enhancers	Spleen	Spleen
34	chr11:72394000-72413800	Strong transcription	Fetal Intestine Large	intestine
35	chr11:72394000-72414600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:72394000-72426800	Strong transcription	Thymus	Thymus
37	chr11:72394200-72395600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:72394200-72395800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:72394200-72408000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:72394200-72423600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr11:72394200-72425800	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr11:72394200-72429000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr11:72394400-72395800	Strong transcription	Brain Substantia Nigra	brain
44	chr11:72394400-72396400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:72394400-72399000	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr11:72394400-72412000	Strong transcription	GM12878-XiMat	blood
47	chr11:72394400-72423200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:72394400-72423800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr11:72394400-72424400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:72394600-72395600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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