Variant report

Variant	rs6682412
Chromosome Location	chr1:223932185-223932186
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223907255..223908800-chr1:223930400..223932243,2	MCF-7	breast:
2	chr1:223931292..223932836-chr1:224033167..224035727,2	K562	blood:
3	chr1:223931041..223933395-chr1:223937050..223938620,2	K562	blood:
4	chr1:223908483..223912094-chr1:223930572..223933646,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10915702	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10915707	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10915715	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12066704	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12066829	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12066831	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12069561	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12070057	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1222134	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1222138	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1222140	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1222141	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12562109	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12563291	0.86[EUR][1000 genomes]
rs12563637	0.83[EUR][1000 genomes]
rs12563713	0.84[EUR][1000 genomes]
rs17597	0.86[EUR][1000 genomes]
rs17598	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17600	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28370069	0.82[EUR][1000 genomes]
rs3738373	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3738374	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3738375	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3767716	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3767717	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3767718	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59248553	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59275322	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6665485	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674541	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674846	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs751609	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7555226	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs898876	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs898877	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv520609	chr1:223931411-223947081	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv521758	chr1:223931411-223954080	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:223915400-223933000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:223915400-223936200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:223916600-223932600	Weak transcription	Fetal Brain Female	brain
5	chr1:223919200-223935600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:223919200-223936200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:223921200-223932800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:223921200-223936000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:223921600-223932800	Weak transcription	Liver	Liver
10	chr1:223921600-223936600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:223921800-223933400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:223921800-223935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:223921800-223936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:223922200-223934600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:223922200-223935600	Weak transcription	Fetal Brain Male	brain
16	chr1:223922800-223934800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:223925200-223934600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:223925400-223934800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:223926800-223932800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:223927400-223933000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:223927800-223935400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:223928000-223932800	Weak transcription	Esophagus	oesophagus
23	chr1:223928000-223933200	Weak transcription	Psoas Muscle	Psoas
24	chr1:223928000-223935400	Weak transcription	Small Intestine	intestine
25	chr1:223928000-223935600	Weak transcription	Right Atrium	heart
26	chr1:223928000-223936400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:223928200-223933400	Weak transcription	K562	blood
28	chr1:223928400-223936200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:223929000-223934800	Weak transcription	Fetal Kidney	kidney
30	chr1:223929400-223932200	Genic enhancers	A549	lung
31	chr1:223929800-223935200	Weak transcription	Fetal Heart	heart
32	chr1:223930000-223933000	Weak transcription	Stomach Mucosa	stomach
33	chr1:223930000-223935000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:223930200-223932800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:223930200-223934800	Strong transcription	Fetal Stomach	stomach
36	chr1:223930200-223935000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:223930200-223935400	Strong transcription	Fetal Intestine Small	intestine
38	chr1:223930200-223935600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:223930400-223934000	Genic enhancers	Lung	lung
40	chr1:223930400-223935200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:223930400-223935400	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr1:223930400-223935800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:223930400-223935800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:223930400-223936000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:223930600-223933400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:223930600-223934800	Strong transcription	NHEK	skin
47	chr1:223930600-223935000	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr1:223930600-223935200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:223930600-223935200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:223930600-223935400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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