Variant report

Variant	rs1205259
Chromosome Location	chr11:65392695-65392696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:65392620-65392770	HBMEC	blood vessel:	n/a	n/a
2	CTCF	chr11:65392580-65392730	K562	blood:	n/a	n/a
3	POLR2A	chr11:65392331-65392787	HepG2	liver:	n/a	n/a
4	CTCF	chr11:65392614-65392773	GM12892	blood:	n/a	n/a
5	CTCF	chr11:65392615-65392736	GM12891	blood:	n/a	n/a
6	POLR2A	chr11:65391418-65392978	GM12878	blood:	n/a	n/a
7	CTCF	chr11:65392571-65392793	K562	blood:	n/a	n/a
8	POLR2A	chr11:65392267-65392923	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:65391853-65392948	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr11:65390348-65392976	GM12892	blood:	n/a	n/a
11	CTCF	chr11:65392638-65392740	MCF-7	breast:	n/a	n/a
12	POLR2A	chr11:65392311-65392860	HL-60	blood:	n/a	n/a
13	CTCF	chr11:65392640-65392790	A549	lung:	n/a	n/a
14	CTCF	chr11:65392684-65392745	GM19238	blood:	n/a	n/a
15	CTCF	chr11:65392619-65392770	K562	blood:	n/a	n/a
16	CTCF	chr11:65392636-65392743	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:65392512-65392725	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr11:65392688-65392886	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:65392626-65393008	K562	blood:	n/a	n/a
20	CTCF	chr11:65392682-65392719	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr11:65392643-65392748	K562	blood:	n/a	n/a
22	RAD21	chr11:65392663-65392733	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr11:65392646-65392706	GM19239	blood:	n/a	n/a
24	CTCF	chr11:65392570-65392914	K562	blood:	n/a	n/a
25	RAD21	chr11:65392636-65392753	K562	blood:	n/a	n/a
26	POLR2A	chr11:65391878-65395319	K562	blood:	n/a	n/a
27	CTCF	chr11:65392631-65392763	MCF-7	breast:	n/a	n/a
28	CTCF	chr11:65392617-65392735	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr11:65392632-65392751	MCF-7	breast:	n/a	n/a
30	POLR2A	chr11:65392320-65392905	K562	blood:	n/a	n/a
31	CTCF	chr11:65392643-65392715	MCF-7	breast:	n/a	n/a
32	CTCF	chr11:65392636-65392749	MCF-7	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65391012..65395205-chr11:65623558..65626894,4	MCF-7	breast:
2	chr11:65319428..65321509-chr11:65390618..65393221,2	MCF-7	breast:

No data

Variant related genes	Relation type
PCNXL3	TF binding region
ENSG00000172732	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000172757	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10896027	0.82[EUR][1000 genomes]
rs10896043	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs11227248	0.81[EUR][1000 genomes]
rs11227249	0.84[EUR][1000 genomes]
rs11227250	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11227261	0.85[CHB][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227284	0.80[ASN][1000 genomes]
rs11227288	0.80[ASN][1000 genomes]
rs11227302	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs1151488	1.00[CHB][hapmap]
rs1193851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12281400	0.87[ASN][1000 genomes]
rs1784223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1787034	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2298615	0.85[CHB][hapmap]
rs2448490	0.90[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs2509948	0.91[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs3372	0.85[CHB][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs34007146	0.87[ASN][1000 genomes]
rs34462081	0.82[EUR][1000 genomes]
rs4930156	0.91[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs4930304	0.89[CHD][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs494003	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs578056	0.80[ASN][1000 genomes]
rs58950470	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7122657	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7944860	1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
2	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
3	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
4	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription 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 miRNA target site	972 gene(s)	inside rSNPs	diseases
5	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
6	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
7	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
8	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
9	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
10	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
11	nsv468599	chr11:65335705-65427346	ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
12	nsv555213	chr11:65335705-65427346	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
13	nsv897732	chr11:65335705-65427346	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
14	nsv468600	chr11:65335705-65431360	Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
15	nsv555214	chr11:65335705-65431360	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
16	nsv897733	chr11:65335705-65431360	Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
17	nsv897734	chr11:65335705-65436888	Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
18	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
19	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription 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	227 gene(s)	inside rSNPs	diseases
20	nsv897746	chr11:65349756-65427346	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
21	nsv897747	chr11:65353906-65481166	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
22	esv1831135	chr11:65387352-65420872	Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	43 gene(s)	inside rSNPs	diseases
23	nsv897748	chr11:65392695-65466911	Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1205259	SLC22A10	cis	parietal	SCAN
rs1205259	RNASEH2C	cis	parietal	SCAN
rs1205259	SIPA1	cis	cerebellum	SCAN
rs1205259	ZBTB3	cis	parietal	SCAN
rs1205259	SLC22A9	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65384400-65402200	Weak transcription	Fetal Kidney	kidney
2	chr11:65384600-65398800	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr11:65384600-65402000	Weak transcription	Psoas Muscle	Psoas
4	chr11:65384800-65393600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr11:65384800-65393600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:65384800-65394000	Weak transcription	Stomach Mucosa	stomach
7	chr11:65384800-65399600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:65384800-65399600	Strong transcription	Ovary	ovary
9	chr11:65384800-65399800	Strong transcription	Osteobl	bone
10	chr11:65384800-65404400	Weak transcription	Fetal Heart	heart
11	chr11:65384800-65404600	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr11:65384800-65404600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr11:65384800-65404600	Strong transcription	Thymus	Thymus
14	chr11:65384800-65404800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:65384800-65404800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:65385000-65393200	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr11:65385000-65393200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:65385000-65393400	Strong transcription	Brain Hippocampus Middle	brain
19	chr11:65385000-65393600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:65385000-65393600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr11:65385000-65393600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:65385000-65396600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr11:65385000-65396600	Weak transcription	Fetal Brain Male	brain
24	chr11:65385000-65398000	Strong transcription	HMEC	breast
25	chr11:65385000-65398600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:65385000-65399600	Strong transcription	Rectal Smooth Muscle	rectum
27	chr11:65385000-65404200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr11:65385000-65404200	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:65385000-65404200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:65385000-65404400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:65385000-65404400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:65385000-65404400	Strong transcription	Fetal Stomach	stomach
33	chr11:65385000-65404600	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr11:65385000-65404600	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:65385000-65404800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:65385000-65405000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:65385000-65405000	Strong transcription	Brain Germinal Matrix	brain
38	chr11:65385000-65405000	Strong transcription	Fetal Brain Female	brain
39	chr11:65385000-65405000	Strong transcription	Fetal Intestine Small	intestine
40	chr11:65385200-65393200	Strong transcription	Pancreas	Pancrea
41	chr11:65385200-65393200	Weak transcription	HSMM	muscle
42	chr11:65385200-65393400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr11:65385200-65393400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr11:65385200-65393400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:65385200-65393600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:65385200-65393600	Strong transcription	Brain Substantia Nigra	brain
47	chr11:65385200-65393600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr11:65385200-65393600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr11:65385200-65398000	Strong transcription	Right Ventricle	heart
50	chr11:65385200-65399400	Strong transcription	Colonic Mucosa	Colon

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