Variant report

Variant	rs12292463
Chromosome Location	chr11:48116141-48116142
allele	C/G
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	RUNX3	chr11:48115219-48116164	GM12878	blood:	n/a	n/a
2	FOXA2	chr11:48115793-48116181	HepG2	liver:	n/a	n/a
3	NFIC	chr11:48115759-48116252	HepG2	liver:	n/a	n/a
4	NFIC	chr11:48115171-48116218	GM12878	blood:	n/a	chr11:48115692-48115709 chr11:48115692-48115708
5	HNF4A	chr11:48115772-48116153	HepG2	liver:	n/a	chr11:48116037-48116052 chr11:48116037-48116052 chr11:48116037-48116052 chr11:48116037-48116052 chr11:48116039-48116052 chr11:48116039-48116052 chr11:48116038-48116052 chr11:48116037-48116052 chr11:48116039-48116051 chr11:48116039-48116051 chr11:48116038-48116051 chr11:48116039-48116052 chr11:48116036-48116054
6	HNF4A	chr11:48115867-48116277	HepG2	liver:	n/a	chr11:48116037-48116052 chr11:48116037-48116052 chr11:48116037-48116052 chr11:48116174-48116189 chr11:48116037-48116052 chr11:48116039-48116052 chr11:48116039-48116052 chr11:48116038-48116052 chr11:48116037-48116052 chr11:48116039-48116051 chr11:48116039-48116051 chr11:48116038-48116051 chr11:48116039-48116052 chr11:48116036-48116054
7	EP300	chr11:48115675-48116261	HepG2	liver:	n/a	n/a
8	FOXA1	chr11:48115816-48116241	HepG2	liver:	n/a	n/a
9	FOXA1	chr11:48115813-48116255	HepG2	liver:	n/a	n/a
10	SP1	chr11:48115797-48116244	HepG2	liver:	n/a	n/a
11	HNF4G	chr11:48115851-48116258	HepG2	liver:	n/a	chr11:48116037-48116052 chr11:48116037-48116052 chr11:48116037-48116052 chr11:48116174-48116189 chr11:48116037-48116052 chr11:48116039-48116052 chr11:48116039-48116052 chr11:48116038-48116052 chr11:48116039-48116051 chr11:48116039-48116051 chr11:48116038-48116053 chr11:48116038-48116051 chr11:48116039-48116052 chr11:48116036-48116054
12	ARID3A	chr11:48114969-48116284	HepG2	liver:	n/a	n/a
13	EP300	chr11:48115853-48116248	HepG2	liver:	n/a	n/a
14	TEAD4	chr11:48115714-48116320	HepG2	liver:	n/a	n/a
15	EP300	chr11:48115731-48116281	HepG2	liver:	n/a	n/a
16	HDAC2	chr11:48115825-48116210	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
MIR3161	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11039489	0.87[YRI][hapmap]
rs11039492	0.88[YRI][hapmap]
rs11039525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11039526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11039554	1.00[YRI][hapmap]
rs12272204	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12272503	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12273331	1.00[AMR][1000 genomes]
rs12275069	0.88[YRI][hapmap]
rs1228029	1.00[YRI][hapmap]
rs1228051	1.00[YRI][hapmap]
rs12282960	0.88[YRI][hapmap]
rs12283260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12292948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12293503	0.87[YRI][hapmap]
rs12294321	1.00[YRI][hapmap]
rs12294477	1.00[YRI][hapmap]
rs12295345	0.88[YRI][hapmap]
rs2229701	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4547053	1.00[AMR][1000 genomes]
rs922959	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv428573	chr11:48032457-48152344	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
15	nsv897328	chr11:48043053-48901553	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv897329	chr11:48052676-48319974	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv1048554	chr11:48062861-48388686	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
18	nsv1038210	chr11:48068862-48388686	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
19	nsv1052076	chr11:48077864-48702549	ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
20	nsv1053528	chr11:48086151-48125731	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
21	nsv869354	chr11:48088580-48783113	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
22	nsv1045734	chr11:48089315-48893207	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
23	nsv467871	chr11:48106486-48694871	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
24	nsv554211	chr11:48106486-48694871	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
25	nsv948502	chr11:48110043-48891877	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48103600-48122800	Weak transcription	Right Ventricle	heart
2	chr11:48105200-48117400	Weak transcription	NHDF-Ad	bronchial
3	chr11:48105800-48121400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:48108800-48125400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:48109800-48117600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:48110200-48117400	Weak transcription	Spleen	Spleen
7	chr11:48110200-48117800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:48110200-48121200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr11:48110400-48117400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:48110600-48117400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:48110600-48117400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:48110600-48117600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr11:48110600-48117600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:48110600-48117600	Weak transcription	Fetal Kidney	kidney
15	chr11:48110800-48116400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:48110800-48117400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr11:48111000-48125400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:48111400-48116400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:48111400-48121400	Weak transcription	Primary T cells from cord blood	blood
20	chr11:48111600-48118800	Enhancers	Fetal Intestine Large	intestine
21	chr11:48111800-48118800	Enhancers	Brain Anterior Caudate	brain
22	chr11:48111800-48121600	Weak transcription	Primary B cells from cord blood	blood
23	chr11:48112600-48117400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:48112600-48117400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:48112800-48117600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:48112800-48121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:48113000-48117400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:48113000-48118400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:48113200-48117400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr11:48113400-48117400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:48113400-48117600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr11:48113600-48117600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:48113600-48118200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:48113600-48118600	Enhancers	Fetal Intestine Small	intestine
35	chr11:48113800-48125400	Enhancers	Brain Hippocampus Middle	brain
36	chr11:48114000-48118600	Enhancers	Brain Substantia Nigra	brain
37	chr11:48114000-48118800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr11:48114000-48119800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr11:48114200-48117000	Enhancers	Stomach Mucosa	stomach
40	chr11:48114200-48117800	Enhancers	Brain Germinal Matrix	brain
41	chr11:48114200-48118400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr11:48114200-48118400	Enhancers	Brain Angular Gyrus	brain
43	chr11:48114200-48119000	Enhancers	Brain Cingulate Gyrus	brain
44	chr11:48114200-48120000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr11:48114400-48116400	Enhancers	Fetal Lung	lung
46	chr11:48114400-48118200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr11:48114600-48117400	Weak transcription	Placenta	Placenta
48	chr11:48114600-48131400	Weak transcription	Esophagus	oesophagus
49	chr11:48114800-48118200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr11:48114800-48118200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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