Variant report

Variant	rs11231631
Chromosome Location	chr11:63659936-63659937
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	MXI1	chr11:63659688-63660207	IMR90	lung:	n/a	n/a
2	CTCF	chr11:63659920-63660070	HBMEC	blood vessel:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
3	ZNF143	chr11:63659811-63659980	K562	blood:	n/a	n/a
4	CTCF	chr11:63659820-63659970	HCM	heart:	n/a	n/a
5	CTCF	chr11:63659880-63660030	HCFaa	heart:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
6	REST	chr11:63659747-63660080	SK-N-SH	brain:	n/a	chr11:63659911-63659920
7	REST	chr11:63659666-63660152	SK-N-SH	brain:	n/a	chr11:63659911-63659920
8	CTCF	chr11:63659840-63659990	HRPEpiC	eye:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
9	CTCF	chr11:63659840-63659990	HPAF	blood vessel:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
10	EP300	chr11:63659936-63659940	GM12878	blood:	n/a	n/a
11	REST	chr11:63659573-63660250	ECC-1	luminal epithelium:	n/a	chr11:63659911-63659920
12	REST	chr11:63659584-63660197	PFSK-1	brain:	n/a	chr11:63659911-63659920
13	REST	chr11:63659615-63660136	HCT-116	colon:	n/a	chr11:63659911-63659920
14	ZNF384	chr11:63659821-63660085	GM12878	blood:	n/a	n/a
15	REST	chr11:63659697-63660063	H1-hESC	embryonic stem cell:	n/a	chr11:63659911-63659920
16	RUNX3	chr11:63659687-63660113	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:63659601-63659945	HepG2	liver:	n/a	n/a
18	TEAD4	chr11:63659693-63660162	A549	lung:	n/a	n/a
19	REST	chr11:63659788-63659987	GM12878	blood:	n/a	chr11:63659911-63659920
20	REST	chr11:63659593-63660135	PANC-1	pancreas:	n/a	chr11:63659911-63659920
21	REST	chr11:63659671-63660202	MCF-7	breast:	n/a	chr11:63659911-63659920
22	REST	chr11:63659154-63660275	HL-60	blood:	n/a	chr11:63659911-63659920
23	REST	chr11:63659740-63660028	K562	blood:	n/a	chr11:63659911-63659920
24	REST	chr11:63659783-63659987	U87	brain:	n/a	chr11:63659911-63659920
25	REST	chr11:63659775-63659972	SK-N-SH	brain:	n/a	chr11:63659911-63659920
26	REST	chr11:63659590-63660105	MCF-7	breast:	n/a	chr11:63659911-63659920
27	CTCF	chr11:63659900-63660050	HAc	cerebellar:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
28	CTCF	chr11:63659900-63660050	HRE	kidney:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
29	REST	chr11:63659711-63660104	A549	lung:	n/a	chr11:63659911-63659920
30	REST	chr11:63659699-63660101	HCT-116	colon:	n/a	chr11:63659911-63659920
31	REST	chr11:63659213-63660234	ECC-1	luminal epithelium:	n/a	chr11:63659911-63659920
32	CTCF	chr11:63659880-63660030	HA-sp	spinal cord:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
33	CTCF	chr11:63659840-63659990	GM12873	blood:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
34	CTCF	chr11:63659920-63660070	HCPEpiC	choroid plexus:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
35	REST	chr11:63659158-63660192	PFSK-1	brain:	n/a	chr11:63659911-63659920
36	CTCF	chr11:63659900-63660050	HCPEpiC	choroid plexus:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
37	TBL1XR1	chr11:63659796-63659948	GM12878	blood:	n/a	n/a
38	RUNX3	chr11:63659695-63660090	GM12878	blood:	n/a	n/a
39	REST	chr11:63659701-63660101	U87	brain:	n/a	chr11:63659911-63659920
40	REST	chr11:63659701-63660117	U87	brain:	n/a	chr11:63659911-63659920
41	CTCF	chr11:63659820-63659970	HVMF	connective:	n/a	n/a
42	REST	chr11:63659737-63660070	PFSK-1	brain:	n/a	chr11:63659911-63659920
43	ZNF384	chr11:63659797-63660062	K562	blood:	n/a	n/a
44	REST	chr11:63659730-63660055	GM12878	blood:	n/a	chr11:63659911-63659920
45	CTCF	chr11:63659920-63660070	HPF	lung:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
46	CTCF	chr11:63659880-63660030	NHDF-neo	bronchial:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
47	SMC3	chr11:63659927-63659995	GM12878	blood:	n/a	chr11:63659978-63659992
48	CTCF	chr11:63659920-63660070	AG10803	skin:	n/a	chr11:63659976-63659989 chr11:63659979-63659988
49	BATF	chr11:63659771-63660040	GM12878	blood:	n/a	n/a
50	CTCF	chr11:63659860-63660010	AG04449	skin:	n/a	chr11:63659976-63659989 chr11:63659979-63659988

No.	Distal block	Cell Line	Cell type
1	chr11:63656662..63659982-chr11:63664623..63666885,3	MCF-7	breast:
2	chr11:63604952..63606733-chr11:63659369..63661422,2	MCF-7	breast:
3	chr11:63654741..63658030-chr11:63658111..63661032,3	K562	blood:

Variant related genes	Relation type
MARK2	TF binding region
ENSG00000072518	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10897457	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231605	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231615	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231619	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231620	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231621	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11231630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231649	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs11231650	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs11231674	1.00[CHB][hapmap]
rs1188017	1.00[CHB][hapmap]
rs2036271	0.84[TSI][hapmap]
rs3850942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530399	1.00[CHB][hapmap]
rs540741	1.00[CHB][hapmap]
rs61886103	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61886104	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61886106	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61886131	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61886132	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61886133	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61886134	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933791	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947843	1.00[CHB][hapmap]
rs958333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9735314	0.94[EUR][1000 genomes];1.00[ASN][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	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer 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 target site	100 gene(s)	inside rSNPs	diseases
2	nsv468589	chr11:63515752-63713239	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv555180	chr11:63515752-63713239	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv1839119	chr11:63615554-63680052	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv468590	chr11:63639881-63783352	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv555181	chr11:63639881-63783352	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11231631	MS4A12	cis	parietal	SCAN
rs11231631	MS4A6E	cis	parietal	SCAN
rs11231631	FTH1	cis	parietal	SCAN
rs11231631	SCYL1	cis	cerebellum	SCAN
rs11231631	GPR137	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63654800-63664000	Weak transcription	Fetal Brain Male	brain
2	chr11:63655800-63662200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:63655800-63662600	Weak transcription	HSMMtube	muscle
4	chr11:63655800-63664200	Weak transcription	NHDF-Ad	bronchial
5	chr11:63656000-63663400	Weak transcription	Fetal Heart	heart
6	chr11:63656200-63660800	Weak transcription	Hela-S3	cervix
7	chr11:63656200-63662400	Weak transcription	NHLF	lung
8	chr11:63656200-63663600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:63656200-63663600	Weak transcription	Aorta	Aorta
10	chr11:63656200-63664000	Weak transcription	NH-A	brain
11	chr11:63656400-63660800	Weak transcription	A549	lung
12	chr11:63656400-63662200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:63656400-63662200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:63656400-63662200	Weak transcription	Ovary	ovary
15	chr11:63656400-63662800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr11:63656400-63663400	Weak transcription	HSMM	muscle
17	chr11:63656400-63663400	Weak transcription	HUVEC	blood vessel
18	chr11:63656400-63665400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:63656600-63660400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr11:63656600-63662400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:63656600-63662400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:63656600-63662600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr11:63656600-63662600	Weak transcription	Osteobl	bone
24	chr11:63656600-63663800	Weak transcription	Fetal Kidney	kidney
25	chr11:63656800-63660200	Genic enhancers	Brain Anterior Caudate	brain
26	chr11:63656800-63660800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:63656800-63660800	Weak transcription	Fetal Lung	lung
28	chr11:63656800-63662200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr11:63656800-63662600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:63656800-63662600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:63656800-63662800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:63656800-63663400	Weak transcription	Small Intestine	intestine
33	chr11:63656800-63665800	Weak transcription	Psoas Muscle	Psoas
34	chr11:63657000-63660000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:63657000-63660400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr11:63657000-63662400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr11:63657000-63662400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:63657000-63662400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:63657000-63662600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:63657000-63670000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:63657200-63662200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:63657200-63662200	Weak transcription	Adipose Nuclei	Adipose
43	chr11:63657400-63660000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:63657400-63660200	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr11:63657400-63660400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr11:63657400-63662600	Weak transcription	Colon Smooth Muscle	Colon
47	chr11:63657400-63677800	Strong transcription	Dnd41	blood
48	chr11:63657600-63660000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr11:63657600-63660000	Genic enhancers	Fetal Thymus	thymus
50	chr11:63657600-63660400	Genic enhancers	Primary T cells fromperipheralblood	blood

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