Variant report

Variant	rs56002981
Chromosome Location	chr7:38860933-38860934
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38857572..38859924-chr7:38860336..38863164,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10247503	0.80[ASN][1000 genomes]
rs10251912	0.80[ASN][1000 genomes]
rs10254567	0.80[ASN][1000 genomes]
rs10271176	0.80[ASN][1000 genomes]
rs10486677	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10486678	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11971020	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11979824	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12533557	0.80[ASN][1000 genomes]
rs12670221	0.83[ASN][1000 genomes]
rs12672885	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17700262	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17700392	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17700752	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17768153	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17768212	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2074655	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2074657	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2107743	0.80[ASN][1000 genomes]
rs2189855	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2214666	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2240351	0.80[ASN][1000 genomes]
rs2240352	0.81[ASN][1000 genomes]
rs2240353	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2240354	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2286082	0.82[ASN][1000 genomes]
rs2286084	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286087	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286088	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286091	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286094	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2286098	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286104	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286105	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286106	0.80[ASN][1000 genomes]
rs2392598	0.80[ASN][1000 genomes]
rs28548028	0.80[ASN][1000 genomes]
rs3801129	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3801139	0.81[ASN][1000 genomes]
rs3801140	0.81[ASN][1000 genomes]
rs3801141	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3801143	0.80[ASN][1000 genomes]
rs3801146	0.80[ASN][1000 genomes]
rs4723782	0.80[ASN][1000 genomes]
rs4723785	0.80[ASN][1000 genomes]
rs57091471	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61363591	0.81[AFR][1000 genomes]
rs62444078	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62444107	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6972321	0.81[AFR][1000 genomes]
rs733150	0.80[ASN][1000 genomes]
rs73357792	0.83[EUR][1000 genomes]
rs73368205	0.91[EUR][1000 genomes]
rs7785911	0.80[ASN][1000 genomes]
rs7786389	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs886646	0.80[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	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38793400-38861200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:38829400-38864400	Weak transcription	Thymus	Thymus
3	chr7:38829400-38864600	Weak transcription	NHLF	lung
4	chr7:38831000-38871200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr7:38831800-38867800	Weak transcription	Fetal Thymus	thymus
6	chr7:38834400-38863400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:38835200-38865200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:38835600-38862200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:38839800-38871000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:38842000-38865400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:38847400-38869800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:38847800-38862400	Weak transcription	Brain Angular Gyrus	brain
14	chr7:38847800-38866800	Weak transcription	Brain Substantia Nigra	brain
15	chr7:38848000-38861200	Weak transcription	Brain Hippocampus Middle	brain
16	chr7:38848200-38861800	Weak transcription	Brain Anterior Caudate	brain
17	chr7:38850200-38865400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:38850600-38869600	Weak transcription	Stomach Mucosa	stomach
19	chr7:38851600-38867000	Weak transcription	Gastric	stomach
20	chr7:38851800-38862200	Weak transcription	K562	blood
21	chr7:38853000-38861000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr7:38853000-38863600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr7:38854000-38870400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:38854400-38861400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:38855400-38865400	Weak transcription	Osteobl	bone
26	chr7:38855600-38863200	Strong transcription	Primary B cells from cord blood	blood
27	chr7:38855600-38871000	Weak transcription	HepG2	liver
28	chr7:38856000-38865200	Weak transcription	NHDF-Ad	bronchial
29	chr7:38856000-38871000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr7:38856200-38865400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr7:38856200-38871200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:38856800-38865000	Weak transcription	GM12878-XiMat	blood
33	chr7:38856800-38865400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr7:38857200-38861000	Weak transcription	Brain Germinal Matrix	brain
35	chr7:38857200-38863600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:38857200-38867200	Weak transcription	Esophagus	oesophagus
37	chr7:38857400-38861000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:38857400-38862400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:38857400-38862600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr7:38857600-38862000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr7:38857600-38862400	Weak transcription	Fetal Brain Female	brain
42	chr7:38857600-38862400	Weak transcription	A549	lung
43	chr7:38857600-38863600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr7:38857600-38865200	Weak transcription	Placenta	Placenta
45	chr7:38857600-38865800	Weak transcription	HSMMtube	muscle
46	chr7:38857600-38871800	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:38857800-38862400	Weak transcription	Fetal Muscle Leg	muscle
48	chr7:38857800-38863600	Weak transcription	Fetal Lung	lung
49	chr7:38857800-38865000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:38857800-38865200	Weak transcription	Colon Smooth Muscle	Colon

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