Variant report

Variant	rs6604729
Chromosome Location	chr1:224023258-224023259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223913473..223915896-chr1:224022022..224024045,2	K562	blood:
2	chr1:223995561..223997893-chr1:224022146..224025073,2	K562	blood:
3	chr1:224021776..224023617-chr1:224025728..224028035,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10503144	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915715	0.82[EUR][1000 genomes]
rs1153965	0.89[EUR][1000 genomes]
rs12046297	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12059128	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059770	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060361	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080250	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088254	0.94[EUR][1000 genomes]
rs12091841	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563291	0.84[EUR][1000 genomes]
rs12563477	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12563637	0.82[EUR][1000 genomes]
rs12563713	0.86[EUR][1000 genomes]
rs12564557	1.00[ASN][1000 genomes]
rs12565202	1.00[ASN][1000 genomes]
rs12565573	1.00[ASN][1000 genomes]
rs12565967	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566817	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841190	1.00[ASN][1000 genomes]
rs16842162	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842229	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16842257	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842326	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842343	1.00[ASN][1000 genomes]
rs17597	0.84[EUR][1000 genomes]
rs28370069	0.83[EUR][1000 genomes]
rs28370073	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28370074	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28370088	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28370159	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370170	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683843	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36032024	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767716	0.81[EUR][1000 genomes]
rs3885657	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41303996	1.00[ASN][1000 genomes]
rs58774026	1.00[ASN][1000 genomes]
rs61823580	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61823581	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823583	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823585	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823587	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823591	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824003	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824005	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61824008	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604724	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604727	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604728	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604730	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658954	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665485	0.81[EUR][1000 genomes]
rs6678365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682964	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685557	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691315	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694960	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696222	1.00[ASN][1000 genomes]
rs6700366	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73116425	1.00[ASN][1000 genomes]
rs73116447	1.00[ASN][1000 genomes]
rs73116451	1.00[ASN][1000 genomes]
rs73116456	1.00[ASN][1000 genomes]
rs7331	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515821	1.00[ASN][1000 genomes]
rs7528455	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530328	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533551	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535882	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
7	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224002000-224023800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:224007000-224024000	Weak transcription	Fetal Intestine Small	intestine
4	chr1:224009400-224023800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:224010200-224026400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:224014200-224023400	Weak transcription	Thymus	Thymus
7	chr1:224014200-224023400	Weak transcription	Dnd41	blood
8	chr1:224014200-224024400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:224015200-224023800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:224015400-224023600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:224015400-224025000	Weak transcription	Fetal Stomach	stomach
12	chr1:224015800-224024200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:224017600-224026800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:224019000-224026400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:224019400-224023400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr1:224019400-224024800	Enhancers	Brain Hippocampus Middle	brain
17	chr1:224019400-224025400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:224019400-224025600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:224019400-224026400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:224019400-224026400	Enhancers	Primary T cells from cord blood	blood
21	chr1:224019400-224027000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr1:224019600-224024600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:224019600-224024600	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:224019600-224027400	Enhancers	Fetal Heart	heart
25	chr1:224019800-224025400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr1:224019800-224026600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr1:224020000-224024800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr1:224020200-224026400	Enhancers	HUVEC	blood vessel
29	chr1:224020400-224023600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr1:224020400-224025800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:224020600-224023400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:224020600-224023800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:224020600-224023800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:224020600-224024000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:224020600-224024400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:224020600-224024400	Weak transcription	HSMMtube	muscle
37	chr1:224020600-224025000	Weak transcription	Brain Germinal Matrix	brain
38	chr1:224020600-224032400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:224020800-224023400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:224020800-224023400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr1:224020800-224023400	Weak transcription	Fetal Thymus	thymus
42	chr1:224020800-224023400	Weak transcription	Right Atrium	heart
43	chr1:224020800-224023400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:224020800-224023600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:224020800-224023800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:224020800-224023800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:224020800-224023800	Weak transcription	Esophagus	oesophagus
48	chr1:224020800-224023800	Weak transcription	Lung	lung
49	chr1:224020800-224023800	Weak transcription	Right Ventricle	heart
50	chr1:224020800-224024400	Weak transcription	Fetal Muscle Leg	muscle

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