Variant report

Variant	rs7742066
Chromosome Location	chr6:110036116-110036117
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	EP300	chr6:110035481-110036132	SK-N-SH_RA	brain:	n/a	n/a
2	NR2F2	chr6:110035728-110036201	MCF-7	breast:	n/a	chr6:110035752-110035767 chr6:110036105-110036120
3	GATA3	chr6:110035548-110036495	MCF-7	breast:	n/a	chr6:110035741-110035757 chr6:110036120-110036127 chr6:110035745-110035754 chr6:110035738-110035759
4	EP300	chr6:110035686-110036227	SK-N-SH	brain:	n/a	n/a
5	NR2F2	chr6:110035758-110036271	MCF-7	breast:	n/a	chr6:110036105-110036120
6	FOXM1	chr6:110035825-110036171	MCF-7	breast:	n/a	n/a
7	GATA3	chr6:110035841-110036343	MCF-7	breast:	n/a	chr6:110036120-110036127
8	TEAD4	chr6:110035775-110036239	SK-N-SH	brain:	n/a	n/a
9	EP300	chr6:110035089-110036595	SK-N-SH	brain:	n/a	n/a
10	GATA2	chr6:110035400-110036227	SH-SY5Y	brain:	n/a	chr6:110035741-110035757 chr6:110036120-110036127 chr6:110035745-110035754 chr6:110035738-110035759
11	GATA3	chr6:110035752-110036243	SH-SY5Y	brain:	n/a	chr6:110036120-110036127
12	FOXM1	chr6:110035772-110036413	MCF-7	breast:	n/a	n/a
13	GATA3	chr6:110036003-110036164	MCF-7	breast:	n/a	chr6:110036120-110036127
14	GATA3	chr6:110035431-110036450	SK-N-SH	brain:	n/a	chr6:110035741-110035757 chr6:110036120-110036127 chr6:110035745-110035754 chr6:110035738-110035759
15	EP300	chr6:110035807-110036154	MCF-7	breast:	n/a	n/a
16	GATA3	chr6:110035553-110036342	SK-N-SH	brain:	n/a	chr6:110035741-110035757 chr6:110036120-110036127 chr6:110035745-110035754 chr6:110035738-110035759

Variant related genes	Relation type
FIG4	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10659	1.00[CEU][hapmap]
rs10872052	0.81[CHB][hapmap]
rs11153200	0.81[CHB][hapmap]
rs11968485	0.81[CHB][hapmap]
rs12215867	0.81[CHB][hapmap]
rs12524352	0.81[CHB][hapmap]
rs1321327	0.81[CHB][hapmap]
rs13437149	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1406957	0.81[CHB][hapmap]
rs1474959	0.81[CHB][hapmap]
rs1570013	0.81[CHB][hapmap]
rs17070874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17070970	1.00[CEU][hapmap]
rs17070972	1.00[CEU][hapmap]
rs17070984	1.00[CEU][hapmap]
rs2016207	0.81[CHB][hapmap]
rs2076929	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs2145144	0.81[CHB][hapmap]
rs2295835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3823235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4512266	1.00[CEU][hapmap]
rs4523125	0.81[CHB][hapmap]
rs4946992	0.81[CHB][hapmap]
rs6568580	0.81[CHB][hapmap]
rs6568587	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes]
rs6568595	0.81[CHB][hapmap]
rs6900091	0.91[AMR][1000 genomes]
rs6916239	0.86[CHB][hapmap]
rs6917383	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6924269	0.81[CHB][hapmap]
rs6925005	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes]
rs6933729	1.00[CEU][hapmap]
rs73535341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356790	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes]
rs7450970	0.81[CHB][hapmap]
rs7453835	0.81[CHB][hapmap]
rs7740192	0.91[AMR][1000 genomes]
rs7743159	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7744512	1.00[CEU][hapmap]
rs7744981	0.81[CHB][hapmap]
rs7745469	0.81[CHB][hapmap]
rs7749605	0.90[CHB][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7749910	0.81[CHB][hapmap]
rs7761008	0.81[CHB][hapmap]
rs7765916	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7767805	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes]
rs7775092	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs829816	0.81[CHB][hapmap]
rs927127	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9320304	0.81[CHB][hapmap]
rs9372222	0.81[CHB][hapmap]
rs9372225	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9372226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9374095	0.81[CHB][hapmap]
rs9374097	0.81[CHB][hapmap]
rs9374108	0.81[CHB][hapmap]
rs9374110	0.88[CHB][hapmap]
rs9374114	0.81[CHB][hapmap]
rs9374117	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9374121	0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9386813	0.81[CHB][hapmap]
rs9386818	0.81[CHB][hapmap]
rs9386824	0.81[CHB][hapmap]
rs9386826	0.88[CHB][hapmap]
rs9386833	0.91[AMR][1000 genomes]
rs9386835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9386842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9398214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9398215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9400310	0.81[CHB][hapmap]
rs9400316	0.81[CHB][hapmap]
rs9480984	0.81[CHB][hapmap]
rs9480990	0.81[AMR][1000 genomes]
rs9480991	0.81[CHB][hapmap]
rs9481003	0.82[CEU][hapmap]
rs9487171	0.81[CHB][hapmap]
rs9487172	0.81[CHB][hapmap]
rs9487175	0.81[CHB][hapmap]
rs9487176	0.81[CHB][hapmap]
rs9487180	0.81[CHB][hapmap]
rs9487186	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9487193	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487203	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs971432	0.81[CHB][hapmap]
rs9986507	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
2	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
3	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
5	chr6:110013400-110038600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:110024200-110038800	Weak transcription	Thymus	Thymus
9	chr6:110024200-110056400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:110025000-110057000	Weak transcription	Fetal Thymus	thymus
11	chr6:110027000-110038200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:110027000-110040400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:110027000-110052400	Weak transcription	Liver	Liver
14	chr6:110027000-110056400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:110027600-110038600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:110027800-110038200	Weak transcription	Placenta	Placenta
17	chr6:110028000-110036800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:110028000-110038000	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:110028000-110044000	Weak transcription	Brain Angular Gyrus	brain
20	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:110028200-110036200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:110028200-110036200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:110028200-110036800	Weak transcription	Adipose Nuclei	Adipose
24	chr6:110028200-110037600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:110028200-110057200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:110029000-110036600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr6:110033200-110041000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:110034200-110039400	Strong transcription	Primary T cells from cord blood	blood
30	chr6:110034400-110041600	Weak transcription	Brain Substantia Nigra	brain
31	chr6:110034400-110042200	Weak transcription	NHLF	lung
32	chr6:110034400-110044400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:110034400-110060800	Weak transcription	Fetal Stomach	stomach
34	chr6:110034600-110037600	Weak transcription	Fetal Intestine Large	intestine
35	chr6:110034600-110041600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:110034600-110041800	Weak transcription	NHDF-Ad	bronchial
37	chr6:110034600-110046600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:110034600-110056400	Weak transcription	Fetal Brain Female	brain
39	chr6:110034600-110057000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:110034800-110036400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:110034800-110036600	Weak transcription	Primary B cells from cord blood	blood
42	chr6:110034800-110037600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:110034800-110038600	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:110034800-110038800	Weak transcription	Fetal Intestine Small	intestine
45	chr6:110034800-110040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:110034800-110042000	Weak transcription	Lung	lung
47	chr6:110034800-110042400	Weak transcription	Brain Anterior Caudate	brain
48	chr6:110034800-110059000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:110035000-110044000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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