Variant report

Variant	rs12292281
Chromosome Location	chr11:62575223-62575224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62575086-62575475	K562	blood:	n/a	n/a
2	POLR2A	chr11:62575084-62575297	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62565367..62576307-chr11:62617328..62626616,39	K562	blood:
2	chr11:62474806..62478433-chr11:62571000..62575830,4	MCF-7	breast:
3	chr11:62445463..62448140-chr11:62574337..62576991,3	K562	blood:
4	chr11:62574784..62577681-chr14:35871976..35874055,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NXF1-1	chr11:62575154-62575535	ENSG00000269463.1

No data

Variant related genes	Relation type
NXF1	TF binding region
ENSG00000255717	Chromatin interaction
ENSG00000100906	Chromatin interaction
ENSG00000162191	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000162188	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11231220	1.00[AMR][1000 genomes]
rs12270342	0.88[LWK][hapmap];0.96[MKK][hapmap];1.00[AMR][1000 genomes]
rs12274689	1.00[YRI][hapmap]
rs12288417	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12290152	0.88[LWK][hapmap];0.96[MKK][hapmap];1.00[AMR][1000 genomes]
rs12295052	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12295516	1.00[AMR][1000 genomes]
rs28400288	1.00[AMR][1000 genomes]
rs56994557	1.00[AMR][1000 genomes]
rs58003814	1.00[AMR][1000 genomes]
rs58505493	1.00[AMR][1000 genomes]
rs58792209	1.00[AMR][1000 genomes]
rs59143369	1.00[AMR][1000 genomes]
rs61088491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73483955	1.00[AMR][1000 genomes]
rs73483965	1.00[AMR][1000 genomes]
rs73483978	1.00[AMR][1000 genomes]
rs73485621	1.00[AMR][1000 genomes]
rs73485634	1.00[AMR][1000 genomes]
rs73485689	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487820	1.00[AMR][1000 genomes]
rs73487823	1.00[AMR][1000 genomes]
rs73487824	1.00[AMR][1000 genomes]
rs73487852	1.00[AMR][1000 genomes]
rs73487868	1.00[AMR][1000 genomes]
rs73502144	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong 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	1401 gene(s)	inside rSNPs	diseases
4	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' 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	489 gene(s)	inside rSNPs	diseases
5	nsv897623	chr11:62438819-62603916	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	215 gene(s)	inside rSNPs	diseases
6	nsv508636	chr11:62547114-62644458	Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1195 gene(s)	inside rSNPs	diseases
7	nsv1051308	chr11:62564713-62673136	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
8	nsv541058	chr11:62564713-62673136	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62573400-62587000	Weak transcription	Gastric	stomach
2	chr11:62573400-62587200	Weak transcription	Ovary	ovary
3	chr11:62573400-62591400	Weak transcription	Stomach Mucosa	stomach
4	chr11:62573600-62576200	Enhancers	NHLF	lung
5	chr11:62573600-62587200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:62573800-62576200	Strong transcription	Fetal Stomach	stomach
7	chr11:62573800-62576200	Enhancers	HUVEC	blood vessel
8	chr11:62573800-62582000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr11:62573800-62582200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:62573800-62583400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr11:62573800-62587000	Weak transcription	Brain Anterior Caudate	brain
12	chr11:62573800-62588600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:62573800-62589000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:62573800-62589800	Weak transcription	A549	lung
15	chr11:62574000-62575400	Genic enhancers	Fetal Muscle Leg	muscle
16	chr11:62574000-62576000	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr11:62574000-62580600	Weak transcription	Primary T cells from cord blood	blood
18	chr11:62574000-62580600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr11:62574000-62581000	Weak transcription	Adipose Nuclei	Adipose
20	chr11:62574000-62583400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr11:62574000-62583400	Weak transcription	Colon Smooth Muscle	Colon
22	chr11:62574000-62584600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr11:62574000-62585400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr11:62574000-62586800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:62574000-62586800	Weak transcription	Brain Angular Gyrus	brain
26	chr11:62574000-62587000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr11:62574000-62587000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:62574000-62588400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr11:62574000-62589200	Weak transcription	Aorta	Aorta
30	chr11:62574000-62590000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:62574000-62590400	Weak transcription	Fetal Kidney	kidney
32	chr11:62574000-62591000	Weak transcription	Fetal Brain Male	brain
33	chr11:62574000-62591400	Weak transcription	Small Intestine	intestine
34	chr11:62574200-62575400	Strong transcription	Fetal Brain Female	brain
35	chr11:62574200-62575400	Strong transcription	Thymus	Thymus
36	chr11:62574200-62578600	Weak transcription	HepG2	liver
37	chr11:62574200-62580800	Weak transcription	NH-A	brain
38	chr11:62574200-62583200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:62574200-62583200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr11:62574200-62583200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr11:62574200-62583400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:62574200-62583400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr11:62574200-62583400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr11:62574200-62583800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr11:62574200-62583800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:62574200-62585200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:62574200-62586000	Weak transcription	Brain Hippocampus Middle	brain
48	chr11:62574200-62586800	Weak transcription	Brain Substantia Nigra	brain
49	chr11:62574200-62587200	Weak transcription	Right Ventricle	heart
50	chr11:62574200-62587800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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