Variant report

Variant	rs2282612
Chromosome Location	chr11:101785248-101785249
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	chr11:101783182-101787393	HUVEC	blood vessel:	n/a	n/a
2	ZNF143	chr11:101785197-101786170	H1-hESC	embryonic stem cell:	n/a	n/a
3	SMC3	chr11:101785243-101786305	Hela-S3	cervix:	n/a	n/a
4	REST	chr11:101784753-101786412	H1-neurons	neurons:	n/a	chr11:101785813-101785826
5	MXI1	chr11:101784875-101787419	SK-N-SH	brain:	n/a	chr11:101786649-101786664
6	POLR2A	chr11:101785139-101787012	Raji	blood:	n/a	n/a
7	SMARCC1	chr11:101785091-101786342	Hela-S3	cervix:	n/a	n/a
8	NFYA	chr11:101785205-101786126	Hela-S3	cervix:	n/a	chr11:101785667-101785682 chr11:101785667-101785682 chr11:101785668-101785682
9	NFYB	chr11:101784864-101786094	Hela-S3	cervix:	n/a	chr11:101785667-101785682 chr11:101785669-101785684 chr11:101785667-101785682 chr11:101785668-101785682
10	USF2	chr11:101785147-101785317	Hela-S3	cervix:	n/a	n/a
11	MAZ	chr11:101785207-101786276	Hela-S3	cervix:	n/a	n/a
12	NFYB	chr11:101785045-101785879	GM12878	blood:	n/a	chr11:101785667-101785682 chr11:101785669-101785684 chr11:101785667-101785682 chr11:101785668-101785682
13	POLR2A	chr11:101785127-101785328	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr11:101785246-101786351	HUVEC	blood vessel:	n/a	n/a
15	RFX5	chr11:101785128-101786616	Hela-S3	cervix:	n/a	n/a
16	KAP1	chr11:101784988-101787159	HEK293	kidney:	n/a	n/a
17	MAZ	chr11:101784293-101787136	IMR90	lung:	n/a	n/a
18	SETDB1	chr11:101785199-101786119	U2OS	brain:	n/a	chr11:101785293-101785317
19	POLR2A	chr11:101785095-101785258	ProgFib	skin:	n/a	n/a
20	ZNF263	chr11:101785087-101786282	HEK293-T-REx	kidney:	n/a	chr11:101785944-101785953 chr11:101785712-101785721
21	EBF1	chr11:101785241-101786000	GM12878	blood:	n/a	chr11:101785610-101785620 chr11:101785611-101785620 chr11:101785609-101785622 chr11:101785609-101785620
22	POLR2A	chr11:101784846-101786865	HUVEC	blood vessel:	n/a	n/a
23	KAP1	chr11:101784998-101786966	U2OS	brain:	n/a	n/a
24	RCOR1	chr11:101785101-101786296	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr11:101785240-101785390	HMEC	breast:	n/a	n/a
26	MXI1	chr11:101784974-101786444	IMR90	lung:	n/a	n/a
27	NRF1	chr11:101785047-101786370	SK-N-SH	brain:	n/a	n/a
28	CTCF	chr11:101785140-101785290	AG10803	skin:	n/a	n/a
29	POLR2A	chr11:101785200-101786776	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
KIAA1377	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1004352	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10791545	0.87[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10791546	0.83[AMR][1000 genomes]
rs10895220	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895224	0.87[YRI][hapmap]
rs10895228	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10895231	0.87[CHB][hapmap];0.81[AMR][1000 genomes]
rs11225049	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11225080	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11225087	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11225093	0.87[CHB][hapmap];0.83[AMR][1000 genomes]
rs12281520	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1274898	0.80[AMR][1000 genomes]
rs12787877	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12802591	0.87[ASW][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1298710	0.84[AMR][1000 genomes]
rs1372414	0.87[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap]
rs1441929	0.87[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs1622630	0.82[AMR][1000 genomes]
rs1661409	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1661410	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1661411	0.87[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs1783740	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2119734	0.87[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59927719	0.89[ASN][1000 genomes]
rs6590940	0.81[AMR][1000 genomes]
rs6590941	0.87[CHB][hapmap];0.83[AMR][1000 genomes]
rs7105709	0.94[ASW][hapmap];0.88[CEU][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7107662	0.88[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7122772	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs975810	0.87[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]

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	nsv1052159	chr11:101439655-101853293	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1051457	chr11:101446705-101837650	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv832250	chr11:101617934-101804020	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3362945	chr11:101736547-102114246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2282612	MMP7	cis	parietal	SCAN
rs2282612	KIAA1377	cis	cerebellum	SCAN
rs2282612	KIAA1377	cis	parietal	SCAN
rs2282612	C11orf70	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101784000-101785400	Weak transcription	Gastric	stomach
2	chr11:101784200-101785600	Flanking Active TSS	Osteobl	bone
3	chr11:101784600-101785600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:101784800-101785400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:101784800-101785400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr11:101784800-101785400	Flanking Active TSS	A549	lung
7	chr11:101784800-101786400	ZNF genes & repeats	Fetal Brain Male	brain
8	chr11:101784800-101786600	Active TSS	Rectal Smooth Muscle	rectum
9	chr11:101784800-101787800	Active TSS	Aorta	Aorta
10	chr11:101785000-101785400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr11:101785000-101785400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr11:101785000-101785400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:101785000-101785400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr11:101785000-101785400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr11:101785000-101785400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr11:101785000-101785400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr11:101785000-101785400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
18	chr11:101785000-101785400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
19	chr11:101785000-101785400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr11:101785000-101785400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr11:101785000-101785400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:101785000-101785400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:101785000-101785400	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr11:101785000-101785400	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr11:101785000-101785400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr11:101785000-101785400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr11:101785000-101785400	Flanking Active TSS	Fetal Brain Female	brain
28	chr11:101785000-101785400	Flanking Active TSS	Fetal Heart	heart
29	chr11:101785000-101785400	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr11:101785000-101785400	Enhancers	Placenta Amnion	Placenta Amnion
31	chr11:101785000-101785600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr11:101785000-101785600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr11:101785000-101785600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr11:101785000-101785600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr11:101785000-101785600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr11:101785000-101785600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr11:101785000-101785600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr11:101785000-101785600	Flanking Active TSS	Fetal Lung	lung
39	chr11:101785000-101785600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr11:101785000-101785600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr11:101785000-101785600	Flanking Active TSS	Dnd41	blood
42	chr11:101785000-101785600	Flanking Active TSS	Hela-S3	cervix
43	chr11:101785000-101785600	Flanking Active TSS	HMEC	breast
44	chr11:101785000-101785600	Flanking Active TSS	HUVEC	blood vessel
45	chr11:101785000-101785600	Flanking Active TSS	NH-A	brain
46	chr11:101785000-101785800	Active TSS	Brain Germinal Matrix	brain
47	chr11:101785000-101786400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:101785000-101786400	Active TSS	Psoas Muscle	Psoas
49	chr11:101785000-101786800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:101785000-101787000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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