Variant report

Variant	rs56743740
Chromosome Location	chr7:66313137-66313138
allele	A/C
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	MYC	chr7:66313077-66313781	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:66310807..66313244-chr7:66448820..66450934,2	MCF-7	breast:
2	chr7:66308221..66311838-chr7:66312285..66316374,5	K562	blood:
3	chr7:66312126..66314998-chr7:66385416..66387725,2	MCF-7	breast:

Variant related genes	Relation type
GTF2IRD1P1	TF binding region
ENSG00000232546	TF binding region
ENSG00000230583	Chromatin interaction
ENSG00000106609	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10232188	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10234747	0.82[AFR][1000 genomes]
rs10235334	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10235423	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10236124	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10237309	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10247591	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10250831	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10258628	0.82[AFR][1000 genomes]
rs10264223	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10264873	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10267922	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10269487	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10270138	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10275343	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10275956	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10279240	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10281794	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10479729	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12531365	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12532805	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12532829	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12532843	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12533298	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12533724	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12534188	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12534948	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12536003	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12537176	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12537474	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12538038	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12540371	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1589887	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17138017	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17680606	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1984651	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2077180	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2091315	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293350	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28510688	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28524571	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28560293	0.82[AFR][1000 genomes]
rs28590087	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28729561	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3778907	0.82[AFR][1000 genomes]
rs3778914	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3778916	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4382352	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4617036	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4717326	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4718417	0.82[AFR][1000 genomes]
rs59765110	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60972148	0.82[AFR][1000 genomes]
rs61554495	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465677	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62465679	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465704	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465717	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465731	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465735	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465746	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465749	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62465751	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465753	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62466579	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62466580	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73139941	0.82[AFR][1000 genomes]
rs73140000	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73143914	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7785755	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv981514	chr7:66310139-66366240	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66310400-66337000	Weak transcription	Small Intestine	intestine
2	chr7:66310600-66329200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:66310800-66313200	Weak transcription	NH-A	brain
4	chr7:66310800-66314600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr7:66310800-66324800	Weak transcription	Brain Substantia Nigra	brain
6	chr7:66310800-66331600	Weak transcription	Ovary	ovary
7	chr7:66311000-66313200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:66311000-66313200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:66311000-66313200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:66311000-66313400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr7:66311000-66313400	Weak transcription	A549	lung
12	chr7:66311000-66313800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr7:66311000-66314000	Weak transcription	Fetal Intestine Small	intestine
14	chr7:66311000-66322400	Weak transcription	Placenta	Placenta
15	chr7:66311000-66323400	Weak transcription	Lung	lung
16	chr7:66311000-66323600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:66311000-66323600	Weak transcription	Primary T cells from cord blood	blood
18	chr7:66311000-66324200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr7:66311000-66324400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr7:66311000-66324600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:66311000-66324600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:66311000-66324600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:66311000-66324600	Weak transcription	Left Ventricle	heart
24	chr7:66311000-66324600	Weak transcription	Psoas Muscle	Psoas
25	chr7:66311000-66324800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:66311000-66324800	Weak transcription	Brain Hippocampus Middle	brain
27	chr7:66311000-66324800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr7:66311000-66325200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr7:66311000-66329000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:66311000-66332600	Weak transcription	Colonic Mucosa	Colon
31	chr7:66311000-66339200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:66311000-66345800	Weak transcription	HSMMtube	muscle
33	chr7:66311000-66349400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr7:66311000-66358400	Weak transcription	Brain Anterior Caudate	brain
35	chr7:66311000-66368000	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:66311000-66385200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr7:66311200-66313200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr7:66311200-66313200	Weak transcription	Hela-S3	cervix
39	chr7:66311200-66313200	Weak transcription	NHEK	skin
40	chr7:66311200-66322000	Weak transcription	Liver	Liver
41	chr7:66311200-66322600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr7:66311200-66322800	Weak transcription	Fetal Muscle Leg	muscle
43	chr7:66311200-66323600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr7:66311200-66324000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:66311200-66324200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr7:66311200-66324200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:66311200-66324600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:66311200-66324600	Weak transcription	Esophagus	oesophagus
49	chr7:66311200-66324600	Weak transcription	Pancreas	Pancrea
50	chr7:66311200-66324800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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