Variant report

Variant	rs2136421
Chromosome Location	chr11:119600410-119600411
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	SP4	chr11:119599901-119600427	H1-hESC	embryonic stem cell:	n/a	n/a
2	EGR1	chr11:119600021-119600455	K562	blood:	n/a	chr11:119600227-119600241 chr11:119600163-119600177 chr11:119600033-119600042 chr11:119600150-119600160
3	RAD21	chr11:119599909-119600477	IMR90	lung:	n/a	chr11:119599960-119599970 chr11:119600188-119600207
4	CTCF	chr11:119600397-119600512	Gliobla	brain:	n/a	n/a
5	MTA3	chr11:119599738-119600600	GM12878	blood:	n/a	n/a
6	CTCF	chr11:119599932-119600423	MCF-7	breast:	n/a	chr11:119600191-119600207 chr11:119600185-119600206
7	SMC3	chr11:119599829-119600563	GM12878	blood:	n/a	chr11:119599984-119599994 chr11:119600192-119600206
8	MAX	chr11:119599396-119600501	A549	lung:	n/a	n/a
9	RAD21	chr11:119599872-119600442	H1-hESC	embryonic stem cell:	n/a	chr11:119599960-119599970 chr11:119600188-119600207
10	POLR2A	chr11:119599496-119601082	MCF-7	breast:	n/a	n/a
11	TCF12	chr11:119599661-119600505	ECC-1	luminal epithelium:	n/a	n/a
12	CTCF	chr11:119600394-119600544	NHEK	skin:	n/a	n/a
13	RCOR1	chr11:119599410-119600576	IMR90	lung:	n/a	n/a
14	POLR2A	chr11:119599477-119601050	GM18951	blood:	n/a	n/a
15	EGR1	chr11:119600019-119600458	MCF-7	breast:	n/a	chr11:119600227-119600241 chr11:119600163-119600177 chr11:119600033-119600042 chr11:119600150-119600160
16	BHLHE40	chr11:119599364-119600490	GM12878	blood:	n/a	chr11:119600069-119600085 chr11:119599385-119599401 chr11:119599847-119599863
17	CTCF	chr11:119599975-119600411	H1-hESC	embryonic stem cell:	n/a	chr11:119600191-119600207 chr11:119600185-119600206
18	BACH1	chr11:119599960-119600558	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr11:119599858-119600537	IMR90	lung:	n/a	chr11:119600191-119600207 chr11:119600185-119600206
20	CTCF	chr11:119599863-119600566	GM12892	blood:	n/a	chr11:119600191-119600207 chr11:119600185-119600206
21	RCOR1	chr11:119599863-119600451	GM12878	blood:	n/a	n/a
22	UBTF	chr11:119599494-119600453	K562	blood:	n/a	n/a
23	RAD21	chr11:119599842-119600418	ECC-1	luminal epithelium:	n/a	chr11:119599960-119599970 chr11:119600188-119600207
24	CTCF	chr11:119599796-119600466	K562	blood:	n/a	chr11:119600191-119600207 chr11:119600185-119600206
25	MAX	chr11:119599438-119600466	GM12878	blood:	n/a	n/a
26	POLR2A	chr11:119599662-119601056	HCT-116	colon:	n/a	n/a
27	CTCF	chr11:119600388-119600507	Fibrobl	skin:	n/a	n/a
28	CREB1	chr11:119599408-119600447	HepG2	liver:	n/a	n/a
29	CTCF	chr11:119599818-119601010	HCT-116	colon:	n/a	chr11:119600191-119600207 chr11:119600185-119600206 chr11:119600881-119600890
30	RAD21	chr11:119599908-119600503	MCF-7	breast:	n/a	chr11:119599960-119599970 chr11:119600188-119600207
31	TEAD4	chr11:119599736-119600420	ECC-1	luminal epithelium:	n/a	n/a
32	SIN3A	chr11:119597072-119600964	H1-hESC	embryonic stem cell:	n/a	chr11:119598510-119598523 chr11:119597118-119597129 chr11:119599794-119599805 chr11:119599846-119599857 chr11:119599845-119599858
33	CTCF	chr11:119599421-119601485	SK-N-SH	brain:	n/a	chr11:119600191-119600207 chr11:119600185-119600206 chr11:119600881-119600890
34	CTCF	chr11:119599708-119600966	A549	lung:	n/a	chr11:119600191-119600207 chr11:119600185-119600206 chr11:119600881-119600890
35	ZBTB7A	chr11:119598965-119600670	ECC-1	luminal epithelium:	n/a	n/a
36	RAD21	chr11:119599770-119600752	HCT-116	colon:	n/a	chr11:119599960-119599970 chr11:119600188-119600207
37	MAX	chr11:119599780-119600427	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr11:119599384-119600413	ECC-1	luminal epithelium:	n/a	n/a
39	REST	chr11:119597919-119600693	H1-neurons	neurons:	n/a	chr11:119599848-119599861 chr11:119599304-119599317 chr11:119598617-119598630 chr11:119599848-119599861 chr11:119599845-119599858 chr11:119600480-119600493 chr11:119600483-119600496 chr11:119599290-119599303 chr11:119598510-119598523 chr11:119599302-119599320 chr11:119599040-119599053
40	RELA	chr11:119599785-119600914	GM19099	blood:	n/a	n/a
41	RAD21	chr11:119599786-119600451	HepG2	liver:	n/a	chr11:119599960-119599970 chr11:119600188-119600207
42	ELF1	chr11:119599452-119601161	GM12878	blood:	n/a	chr11:119600483-119600495 chr11:119599527-119599539
43	SIN3A	chr11:119599862-119600463	GM12878	blood:	n/a	n/a
44	POLR2A	chr11:119599368-119601097	MCF-7	breast:	n/a	n/a
45	FOXM1	chr11:119599797-119600456	GM12878	blood:	n/a	n/a
46	POLR2A	chr11:119599556-119601033	GM19099	blood:	n/a	n/a
47	CTCF	chr11:119599855-119600516	Kidney_OC	kidney:	n/a	chr11:119600191-119600207 chr11:119600185-119600206
48	STAT1	chr11:119599938-119600433	GM12878	blood:	n/a	n/a
49	MAZ	chr11:119597671-119601057	IMR90	lung:	n/a	chr11:119598584-119598594 chr11:119598070-119598085 chr11:119598072-119598087 chr11:119598074-119598083 chr11:119598074-119598083 chr11:119598072-119598085 chr11:119598073-119598082 chr11:119598073-119598083 chr11:119598075-119598082 chr11:119598074-119598084 chr11:119598073-119598084 chr11:119598073-119598083 chr11:119598072-119598085 chr11:119598073-119598084 chr11:119598072-119598085
50	CTCF	chr11:119600360-119600510	HCPEpiC	choroid plexus:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:119557449..119558968-chr11:119599043..119600568,2	MCF-7	breast:
2	chr11:119598280..119601010-chr11:119990751..119994590,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTD-2523D13.1.1-1	chr11:119600361-119600563	XLOC_009299
2	lnc-CTD-2523D13.1.1-1	chr11:119600281-119600516	XLOC_009299
3	lnc-CTD-2523D13.1.1-1	chr11:119600356-119600563	XLOC_009299

Variant related genes	Relation type
PVRL1	TF binding region
ENSG00000137699	Chromatin interaction
ENSG00000110400	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10790339	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10892444	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10892445	0.81[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10892446	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217426	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs11217429	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11217430	0.86[EUR][1000 genomes]
rs11217433	0.81[AFR][1000 genomes]
rs11217434	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11217437	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217438	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217440	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217441	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217442	0.82[EUR][1000 genomes]
rs11217448	0.81[EUR][1000 genomes]
rs11607610	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12418662	0.85[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12421434	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12421466	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12786505	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12793075	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12796806	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12797914	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12800445	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1876795	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2136420	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2368936	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35248712	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829260	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245206	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4489755	0.81[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4505073	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4936496	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938718	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938719	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4938720	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58136657	0.82[EUR][1000 genomes]
rs6589770	0.81[EUR][1000 genomes]
rs73006720	0.82[EUR][1000 genomes]
rs7952366	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9666263	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898421	chr11:119499014-119631325	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv898422	chr11:119518006-119601779	Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv898423	chr11:119541332-119659753	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1051769	chr11:119572865-119630769	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1037739	chr11:119592989-119630641	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv3364090	chr11:119598267-119601315	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2136421	SORL1	cis	cerebellum	SCAN
rs2136421	HSPA8	cis	parietal	SCAN
rs2136421	DDX6	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119597200-119600800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr11:119597200-119601000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr11:119597200-119601000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr11:119597400-119600600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:119597400-119600800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr11:119597400-119601000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr11:119597400-119601000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:119597600-119601000	Active TSS	Fetal Kidney	kidney
9	chr11:119597800-119600800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:119597800-119600800	Active TSS	Fetal Brain Female	brain
11	chr11:119597800-119601000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:119597800-119601000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:119598000-119600600	Active TSS	Small Intestine	intestine
14	chr11:119598000-119600600	Active TSS	HSMMtube	muscle
15	chr11:119598000-119600800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:119598000-119600800	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr11:119598000-119600800	Active TSS	A549	lung
18	chr11:119598000-119600800	Active TSS	Hela-S3	cervix
19	chr11:119598000-119601200	Active TSS	Right Atrium	heart
20	chr11:119598200-119600600	Active TSS	Gastric	stomach
21	chr11:119598200-119600800	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr11:119598200-119600800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr11:119598200-119600800	Active TSS	Brain Substantia Nigra	brain
24	chr11:119598200-119601000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:119598200-119601000	Active TSS	Aorta	Aorta
26	chr11:119598400-119600600	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr11:119598400-119600800	Active TSS	Brain Angular Gyrus	brain
28	chr11:119598400-119601000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:119598400-119601000	Active TSS	Psoas Muscle	Psoas
30	chr11:119598400-119601200	Active TSS	NHDF-Ad	bronchial
31	chr11:119598600-119600800	Active TSS	Colon Smooth Muscle	Colon
32	chr11:119598600-119600800	Active TSS	Left Ventricle	heart
33	chr11:119598600-119600800	Active TSS	Lung	lung
34	chr11:119598600-119600800	Active TSS	Ovary	ovary
35	chr11:119598800-119600800	Active TSS	Brain Hippocampus Middle	brain
36	chr11:119598800-119601000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:119599000-119600800	Active TSS	Brain Germinal Matrix	brain
38	chr11:119599000-119601000	Active TSS	NHLF	lung
39	chr11:119599200-119600600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:119599200-119600600	Active TSS	Duodenum Mucosa	Duodenum
41	chr11:119599200-119600600	Active TSS	GM12878-XiMat	blood
42	chr11:119599200-119600800	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr11:119599200-119601200	Active TSS	Right Ventricle	heart
44	chr11:119599400-119600600	Active TSS	Primary T cells from cord blood	blood
45	chr11:119599400-119600600	Bivalent/Poised TSS	Thymus	Thymus
46	chr11:119599400-119601000	Active TSS	Spleen	Spleen
47	chr11:119600000-119600600	Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr11:119600000-119600600	Active TSS	Fetal Lung	lung
49	chr11:119600000-119600600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
50	chr11:119600000-119601000	Enhancers	Fetal Brain Male	brain

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