Variant report

Variant	rs2529400
Chromosome Location	chr7:50774621-50774622
allele	A/G
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	RAD21	chr7:50774163-50774630	Hela-S3	cervix:	n/a	n/a
2	GATA3	chr7:50774247-50774727	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr7:50774211-50774728	MCF-7	breast:	n/a	n/a
4	FOS	chr7:50774041-50774691	MCF10A-Er-Src	breast:	n/a	n/a
5	ZNF217	chr7:50774150-50774662	MCF-7	breast:	n/a	n/a
6	GATA3	chr7:50774361-50774699	MCF-7	breast:	n/a	n/a
7	MYC	chr7:50773943-50774748	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr7:50774098-50774623	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr7:50774063-50774662	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr7:50774108-50774663	MCF10A-Er-Src	breast:	n/a	n/a
11	GATA3	chr7:50773915-50774803	MCF-7	breast:	n/a	chr7:50774788-50774797 chr7:50774788-50774795
12	FOS	chr7:50774081-50774667	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50771946..50774688-chr7:50777766..50780192,2	K562	blood:

Variant related genes	Relation type
GRB10	TF binding region
ENSG00000106070	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1004402	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1019002	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10216232	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1024532	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1548609	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs2011899	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108350	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2190497	0.81[JPT][hapmap]
rs2190501	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190503	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237469	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237481	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237488	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301926	0.83[AMR][1000 genomes]
rs2301927	0.83[AMR][1000 genomes]
rs2329492	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2529404	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2529407	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2529409	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2715102	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715105	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715110	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2715117	0.81[JPT][hapmap]
rs2715118	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2715125	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715128	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2715134	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3800999	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4947432	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4947444	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4947446	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4947804	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4947835	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4947836	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4947837	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4947842	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4947866	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs4947886	0.83[AMR][1000 genomes]
rs4947890	0.83[AMR][1000 genomes]
rs4947891	0.83[AMR][1000 genomes]
rs6593140	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6593142	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6593171	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6945302	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6973119	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6978627	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs757775	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7791286	0.85[CEU][hapmap]
rs886821	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs962508	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs977791	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990358	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50742600-50792000	Weak transcription	Primary T cells from cord blood	blood
2	chr7:50750000-50778600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:50755400-50777000	Weak transcription	Esophagus	oesophagus
4	chr7:50756200-50779200	Weak transcription	Osteobl	bone
5	chr7:50757000-50775000	Weak transcription	Psoas Muscle	Psoas
6	chr7:50758800-50779400	Weak transcription	Fetal Kidney	kidney
7	chr7:50763400-50806800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:50764000-50778800	Weak transcription	HSMM	muscle
9	chr7:50765400-50776800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr7:50765800-50776800	Weak transcription	Brain Angular Gyrus	brain
11	chr7:50765800-50776800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:50765800-50776800	Weak transcription	Fetal Intestine Small	intestine
13	chr7:50765800-50777000	Weak transcription	Fetal Stomach	stomach
14	chr7:50766200-50777600	Weak transcription	Brain Anterior Caudate	brain
15	chr7:50766400-50776800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr7:50766400-50779800	Weak transcription	Brain Germinal Matrix	brain
17	chr7:50766400-50783200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:50766400-50785800	Weak transcription	Small Intestine	intestine
19	chr7:50766600-50779000	Weak transcription	Fetal Lung	lung
20	chr7:50768600-50776600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:50770200-50776800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr7:50770400-50775400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:50770400-50776000	Weak transcription	Brain Substantia Nigra	brain
24	chr7:50770400-50776000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr7:50770400-50776800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:50770400-50776800	Weak transcription	Gastric	stomach
27	chr7:50770400-50777000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr7:50770400-50778000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:50770400-50778000	Weak transcription	Spleen	Spleen
30	chr7:50770400-50778800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:50770400-50779000	Weak transcription	Ovary	ovary
32	chr7:50770600-50779200	Weak transcription	NH-A	brain
33	chr7:50770600-50779200	Weak transcription	NHDF-Ad	bronchial
34	chr7:50770600-50779600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr7:50770600-50779600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr7:50770800-50775000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr7:50771200-50776800	Weak transcription	HSMMtube	muscle
38	chr7:50771400-50777000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr7:50771400-50779600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:50771600-50777600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:50771600-50777600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:50771600-50780200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:50771800-50775400	Weak transcription	HUVEC	blood vessel
44	chr7:50771800-50776600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:50771800-50777800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:50772000-50791600	Weak transcription	K562	blood
47	chr7:50772200-50776800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr7:50773000-50774800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:50773000-50775400	Weak transcription	Pancreas	Pancrea
50	chr7:50773000-50776200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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