Variant report

Variant	rs962554
Chromosome Location	chr6:142734204-142734205
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	NFIC	chr6:142734137-142735300	SK-N-SH	brain:	n/a	n/a
2	EP300	chr6:142734194-142735234	SK-N-SH	brain:	n/a	chr6:142734405-142734412
3	TCF12	chr6:142733768-142735334	SK-N-SH	brain:	n/a	chr6:142734634-142734643
4	TCF12	chr6:142734101-142735272	SK-N-SH	brain:	n/a	chr6:142734634-142734643
5	FOS	chr6:142733812-142735041	MCF10A-Er-Src	breast:	n/a	chr6:142734756-142734767 chr6:142734777-142734788
6	JUND	chr6:142734188-142735196	SK-N-SH	brain:	n/a	chr6:142734777-142734788
7	GATA3	chr6:142733627-142735403	SK-N-SH	brain:	n/a	chr6:142734296-142734303 chr6:142734296-142734303 chr6:142734295-142734305 chr6:142734296-142734303 chr6:142734540-142734553 chr6:142734292-142734308 chr6:142733996-142734017 chr6:142734294-142734307 chr6:142734296-142734305 chr6:142734896-142734904 chr6:142733998-142734014 chr6:142734181-142734197
8	FOSL2	chr6:142734159-142735164	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr6:142733713-142735203	SK-N-SH	brain:	n/a	chr6:142734296-142734303 chr6:142734296-142734303 chr6:142734295-142734305 chr6:142734296-142734303 chr6:142734540-142734553 chr6:142734292-142734308 chr6:142733996-142734017 chr6:142734294-142734307 chr6:142734296-142734305 chr6:142734896-142734904 chr6:142733998-142734014 chr6:142734181-142734197
10	TEAD4	chr6:142734181-142735202	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:142733339..142736237-chr6:142747446..142749492,2	MCF-7	breast:
2	chr6:142733840..142736279-chr6:142738480..142740069,2	MCF-7	breast:
3	chr6:142723359..142725425-chr6:142732733..142734946,2	MCF-7	breast:

Variant related genes	Relation type
GPR126	TF binding region
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1040525	0.91[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1040526	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1342060	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs1360194	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1418201	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs155259	0.88[EUR][1000 genomes]
rs1891308	0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2039986	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2039987	0.89[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs2050157	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2294764	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294771	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs262115	0.81[EUR][1000 genomes]
rs262119	0.88[EUR][1000 genomes]
rs262121	0.88[EUR][1000 genomes]
rs262129	0.88[EUR][1000 genomes]
rs263178	0.86[EUR][1000 genomes]
rs263179	0.86[EUR][1000 genomes]
rs263180	0.88[EUR][1000 genomes]
rs263181	0.88[EUR][1000 genomes]
rs263182	0.88[EUR][1000 genomes]
rs263183	0.88[EUR][1000 genomes]
rs263184	0.88[EUR][1000 genomes]
rs263185	0.85[EUR][1000 genomes]
rs263186	0.88[EUR][1000 genomes]
rs263187	0.88[EUR][1000 genomes]
rs263188	0.88[EUR][1000 genomes]
rs263189	0.88[EUR][1000 genomes]
rs3748069	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817929	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896582	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs611802	0.84[EUR][1000 genomes]
rs6570507	0.84[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6570508	0.90[EUR][1000 genomes]
rs6570509	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6570510	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6909857	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6929442	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6937121	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7741741	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7753012	0.95[CEU][hapmap]
rs7754638	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7755109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7756305	0.95[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes]
rs7763064	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7770386	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7774095	0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7776375	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373346	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389984	0.87[EUR][1000 genomes]
rs9389985	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9389986	0.85[CEU][hapmap];0.91[CHB][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389987	0.90[EUR][1000 genomes]
rs9399401	0.95[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9403380	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9403381	0.84[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9403382	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403383	0.91[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403387	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9496346	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9496369	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9496374	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496392	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs972982	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142708000-142734800	Weak transcription	Esophagus	oesophagus
2	chr6:142712200-142735000	Weak transcription	Fetal Brain Male	brain
3	chr6:142718000-142763200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:142719800-142735400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:142720600-142736800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:142721600-142749200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:142722000-142743400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:142726200-142736000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:142726600-142737400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:142726800-142738000	Weak transcription	Stomach Mucosa	stomach
11	chr6:142727000-142743400	Strong transcription	HepG2	liver
12	chr6:142728400-142736800	Weak transcription	Fetal Intestine Large	intestine
13	chr6:142729200-142743200	Strong transcription	Liver	Liver
14	chr6:142730200-142747600	Weak transcription	Fetal Intestine Small	intestine
15	chr6:142730400-142738200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:142731200-142737000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:142731600-142734800	Weak transcription	Placenta	Placenta
18	chr6:142731600-142737600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:142732600-142734800	Weak transcription	Fetal Lung	lung
20	chr6:142732600-142737000	Weak transcription	Primary T cells from cord blood	blood
21	chr6:142732800-142734800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:142733000-142738600	Enhancers	NHDF-Ad	bronchial
23	chr6:142733200-142734400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr6:142733200-142735800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr6:142733200-142735800	Enhancers	NHEK	skin
26	chr6:142733200-142736000	Enhancers	NHLF	lung
27	chr6:142733400-142735200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:142733400-142735400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:142733400-142735800	Enhancers	NH-A	brain
30	chr6:142733400-142737600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:142733400-142739200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:142733400-142739200	Enhancers	Osteobl	bone
33	chr6:142733600-142734400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:142733600-142734800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:142733600-142735800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:142733600-142735800	Enhancers	HMEC	breast
37	chr6:142733600-142736800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:142733600-142737800	Enhancers	HSMMtube	muscle
39	chr6:142733800-142734800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:142733800-142736800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:142733800-142736800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:142733800-142736800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:142733800-142736800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:142733800-142738600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:142733800-142758000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:142734000-142734400	Enhancers	A549	lung
47	chr6:142734000-142735000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:142734000-142735000	Weak transcription	HSMM	muscle
49	chr6:142734000-142735600	Enhancers	HUVEC	blood vessel
50	chr6:142734200-142734600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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