Variant report

Variant	rs13105156
Chromosome Location	chr4:144256713-144256714
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	JUN	chr4:144256704-144257862	K562	blood:	n/a	n/a
2	YY1	chr4:144256681-144257435	H1-hESC	embryonic stem cell:	n/a	chr4:144257088-144257096 chr4:144257087-144257099
3	TAF1	chr4:144256672-144257785	H1-hESC	embryonic stem cell:	n/a	n/a
4	ELF1	chr4:144256713-144259137	GM12878	blood:	n/a	chr4:144257385-144257397 chr4:144258753-144258766
5	POLR2A	chr4:144256548-144259109	H1-hESC	embryonic stem cell:	n/a	n/a
6	TBP	chr4:144256677-144259046	H1-hESC	embryonic stem cell:	n/a	chr4:144258666-144258677
7	YY1	chr4:144256530-144257529	H1-hESC	embryonic stem cell:	n/a	chr4:144257088-144257096 chr4:144257087-144257099 chr4:144257520-144257529
8	POLR2A	chr4:144256687-144257518	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr4:144256677-144258689	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAZ	chr4:144256618-144259435	IMR90	lung:	n/a	chr4:144257518-144257528 chr4:144256930-144256940
11	MAZ	chr4:144256679-144259076	GM12878	blood:	n/a	chr4:144257518-144257528 chr4:144256930-144256940
12	TAF1	chr4:144256608-144258643	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr4:144256696-144258594	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:124524644..124527323-chr4:144255705..144257566,2	MCF-7	breast:
2	chr4:144104818..144107585-chr4:144256509..144260468,4	MCF-7	breast:
3	chr4:144254658..144259448-chr4:144261105..144264742,6	MCF-7	breast:
4	chr4:144254627..144258395-chr4:144297952..144301828,4	K562	blood:
5	chr4:144256474..144260869-chr4:144433151..144436933,4	K562	blood:
6	chr4:144251943..144253888-chr4:144255920..144257556,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FREM3-6	chr4:144256418-144258970	NONHSAT098553

Variant related genes	Relation type
GAB1	TF binding region
ENSG00000109458	Chromatin interaction
ENSG00000170185	Chromatin interaction
ENSG00000245112	Chromatin interaction
ENSG00000153147	Chromatin interaction
ENSG00000265623	Chromatin interaction
ENSG00000250326	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10025700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12331265	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13133540	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146448	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2323079	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377860	0.81[AFR][1000 genomes]
rs28397211	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28408110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28676298	0.92[AFR][1000 genomes]
rs28846534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300950	1.00[CHB][hapmap]
rs300954	1.00[CHB][hapmap]
rs300955	1.00[CHB][hapmap]
rs34420992	0.85[AMR][1000 genomes]
rs6826079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv3332574	chr4:144239396-144259577	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	nsv1026110	chr4:144239825-144292148	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144256000-144259600	Active TSS	Fetal Kidney	kidney
2	chr4:144256200-144257200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr4:144256200-144259000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:144256400-144257000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:144256400-144257000	Flanking Active TSS	Placenta	Placenta
6	chr4:144256600-144256800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:144256600-144256800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr4:144256600-144256800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:144256600-144256800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr4:144256600-144256800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:144256600-144256800	Active TSS	Brain Germinal Matrix	brain
12	chr4:144256600-144256800	Enhancers	Colonic Mucosa	Colon
13	chr4:144256600-144256800	Enhancers	Fetal Brain Male	brain
14	chr4:144256600-144256800	Active TSS	Fetal Brain Female	brain
15	chr4:144256600-144256800	Enhancers	Right Atrium	heart
16	chr4:144256600-144256800	Enhancers	Small Intestine	intestine
17	chr4:144256600-144256800	Enhancers	Stomach Mucosa	stomach
18	chr4:144256600-144256800	Enhancers	Spleen	Spleen
19	chr4:144256600-144256800	Active TSS	HepG2	liver
20	chr4:144256600-144257000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:144256600-144257000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr4:144256600-144257000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr4:144256600-144257000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr4:144256600-144257000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:144256600-144257000	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr4:144256600-144257000	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr4:144256600-144257000	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr4:144256600-144257000	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr4:144256600-144257000	Flanking Active TSS	Fetal Stomach	stomach
30	chr4:144256600-144257200	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr4:144256600-144257200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:144256600-144257400	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr4:144256600-144257400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr4:144256600-144257600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:144256600-144258600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:144256600-144258600	Active TSS	Fetal Muscle Trunk	muscle
37	chr4:144256600-144258800	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr4:144256600-144258800	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr4:144256600-144258800	Active TSS	Liver	Liver
40	chr4:144256600-144258800	Active TSS	Hela-S3	cervix
41	chr4:144256600-144259000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:144256600-144259000	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr4:144256600-144259000	Active TSS	HMEC	breast
44	chr4:144256600-144259000	Active TSS	HUVEC	blood vessel
45	chr4:144256600-144259000	Active TSS	NH-A	brain
46	chr4:144256600-144259000	Active TSS	NHEK	skin
47	chr4:144256600-144259000	Active TSS	Osteobl	bone
48	chr4:144256600-144259200	Active TSS	H1 Cell Line	embryonic stem cell
49	chr4:144256600-144259200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:144256600-144259200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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