Variant report

Variant	rs13411177
Chromosome Location	chr2:86996135-86996136
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	chr2:86996132-86996169	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86995678..86997239-chr2:87001923..87004036,2	K562	blood:
2	chr2:86991045..86994213-chr2:86994492..86997547,4	K562	blood:

Variant related genes	Relation type
RMND5A	TF binding region
ENSG00000153561	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10175293	0.90[ASN][1000 genomes]
rs10177148	1.00[EUR][1000 genomes]
rs10197244	0.90[ASN][1000 genomes]
rs10201581	0.90[ASN][1000 genomes]
rs10207306	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10207541	1.00[EUR][1000 genomes]
rs10208436	0.90[ASN][1000 genomes]
rs12476889	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12477946	1.00[EUR][1000 genomes]
rs13410422	0.90[ASN][1000 genomes]
rs13412314	1.00[EUR][1000 genomes]
rs13413566	0.90[ASN][1000 genomes]
rs13416756	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13430105	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13431959	0.90[ASN][1000 genomes]
rs2367368	0.90[ASN][1000 genomes]
rs28662199	0.90[ASN][1000 genomes]
rs28851847	0.90[ASN][1000 genomes]
rs28889570	0.90[ASN][1000 genomes]
rs4402760	0.90[ASN][1000 genomes]
rs6735599	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349247	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570057	0.90[ASN][1000 genomes]
rs7577266	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv10063	chr2:86940988-87084360	Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002420	chr2:86948835-87172715	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv874472	chr2:86961252-87071474	Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1008817	chr2:86970406-87172715	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv14382	chr2:86972214-87174121	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv997982	chr2:86972834-87105864	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1007746	chr2:86972834-87172715	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv458585	chr2:86974318-87108211	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv582373	chr2:86974318-87108211	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv1007307	chr2:86974563-87055214	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv535809	chr2:86974563-87055214	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv1003748	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv535810	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv1004572	chr2:86975514-87082883	Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
16	nsv535811	chr2:86975514-87082883	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86968600-86997600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:86969200-86997800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:86969400-86997800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:86970000-87002000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:86974200-87004200	Weak transcription	Small Intestine	intestine
6	chr2:86974800-86999800	Weak transcription	Stomach Mucosa	stomach
7	chr2:86975400-87003000	Weak transcription	Fetal Brain Male	brain
8	chr2:86975800-86999600	Weak transcription	NHLF	lung
9	chr2:86975800-87006600	Weak transcription	NH-A	brain
10	chr2:86977600-86997800	Weak transcription	HSMMtube	muscle
11	chr2:86978200-87003000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:86980400-87001400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:86980600-87002800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:86981000-86997000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:86981200-86997600	Weak transcription	HUVEC	blood vessel
16	chr2:86981400-86997000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:86981400-87004600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:86981600-87007000	Weak transcription	NHDF-Ad	bronchial
19	chr2:86982000-86999200	Weak transcription	Colonic Mucosa	Colon
20	chr2:86982000-87001000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:86982200-86997200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:86984200-87006000	Weak transcription	Ovary	ovary
23	chr2:86984600-87007600	Weak transcription	Psoas Muscle	Psoas
24	chr2:86987000-86997400	Weak transcription	Brain Germinal Matrix	brain
25	chr2:86987800-86997600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:86988800-86997400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:86988800-87006200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:86991600-87004600	Strong transcription	Primary B cells from cord blood	blood
29	chr2:86991800-86999600	Strong transcription	HepG2	liver
30	chr2:86991800-87004200	Strong transcription	Primary T cells from cord blood	blood
31	chr2:86991800-87004600	Genic enhancers	Fetal Thymus	thymus
32	chr2:86992000-87003400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:86992200-86998800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:86992200-87003200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:86992200-87004400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr2:86992200-87004400	Strong transcription	Dnd41	blood
37	chr2:86992200-87004600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:86992200-87004600	Strong transcription	Fetal Intestine Large	intestine
39	chr2:86992400-86997000	Weak transcription	Brain Angular Gyrus	brain
40	chr2:86992400-87000600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:86992400-87001400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:86992400-87003800	Strong transcription	Fetal Intestine Small	intestine
43	chr2:86992400-87004000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr2:86992400-87004400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:86992400-87004600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:86992400-87004800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr2:86992600-87002400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:86992600-87003200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:86992600-87003200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:86992600-87003400	Strong transcription	Primary T helper cells PMA-I stimulated	--

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