Variant report

Variant	rs6694960
Chromosome Location	chr1:224001273-224001274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223999460..224001439-chr1:224004268..224006826,2	K562	blood:
2	chr1:223989300..223992010-chr1:223998134..224001519,3	K562	blood:
3	chr1:224000840..224004910-chr1:224006824..224010402,6	K562	blood:
4	chr1:224001116..224004491-chr1:224031166..224035522,4	K562	blood:
5	chr1:223998930..224001381-chr1:224032670..224034728,2	K562	blood:
6	chr1:223998721..224001505-chr1:224009305..224011970,2	K562	blood:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10159015	0.82[EUR][1000 genomes]
rs10465524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10495215	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10495216	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10495217	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10503144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915702	0.81[EUR][1000 genomes]
rs10915707	0.83[EUR][1000 genomes]
rs10915715	0.86[EUR][1000 genomes]
rs1153958	0.82[EUR][1000 genomes]
rs1153965	0.93[EUR][1000 genomes]
rs12046297	0.89[EUR][1000 genomes]
rs12059128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060361	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066704	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12066829	0.81[EUR][1000 genomes]
rs12066831	0.81[EUR][1000 genomes]
rs12069561	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12070057	0.81[EUR][1000 genomes]
rs12080250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088254	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs12091841	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222134	0.83[EUR][1000 genomes]
rs1222138	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1222140	0.81[EUR][1000 genomes]
rs1222141	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12562109	0.83[EUR][1000 genomes]
rs12563291	0.89[EUR][1000 genomes]
rs12563477	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12563637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12563713	0.90[EUR][1000 genomes]
rs12564557	1.00[ASN][1000 genomes]
rs12565202	1.00[ASN][1000 genomes]
rs12565573	1.00[ASN][1000 genomes]
rs12565967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568612	0.85[CEU][hapmap]
rs1629836	1.00[CEU][hapmap]
rs16841190	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16842162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842229	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16842257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842343	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17556570	0.85[CEU][hapmap]
rs17557288	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17557525	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17557623	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17597	0.89[EUR][1000 genomes]
rs17598	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17600	0.83[EUR][1000 genomes]
rs28370069	0.87[EUR][1000 genomes]
rs28370073	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28370074	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28370088	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28370159	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370170	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683843	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36032024	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738373	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs3738374	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs3738375	0.83[EUR][1000 genomes]
rs3767716	0.85[EUR][1000 genomes]
rs3767717	0.83[EUR][1000 genomes]
rs3767718	0.83[EUR][1000 genomes]
rs3885657	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41303996	1.00[ASN][1000 genomes]
rs4653522	0.85[CEU][hapmap]
rs4993742	0.82[CEU][hapmap]
rs58774026	1.00[ASN][1000 genomes]
rs59275322	0.81[EUR][1000 genomes]
rs61823580	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61823581	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823583	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823585	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823587	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823591	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824003	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824005	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61824008	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604727	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604728	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604729	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604730	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658954	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665485	0.85[EUR][1000 genomes]
rs6671245	1.00[CEU][hapmap]
rs6674541	0.81[EUR][1000 genomes]
rs6674846	0.81[EUR][1000 genomes]
rs6678365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682964	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683052	1.00[CEU][hapmap]
rs6685475	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6685557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693372	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6693884	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6696053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6696222	1.00[ASN][1000 genomes]
rs6700366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703104	0.85[CEU][hapmap]
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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515821	1.00[ASN][1000 genomes]
rs751609	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7528455	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549063	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7552702	0.82[EUR][1000 genomes]
rs7555226	0.81[EUR][1000 genomes]
rs898876	0.81[EUR][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	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
8	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:223960600-224001400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:223961800-224004400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:223964400-224008000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:223976800-224003000	Weak transcription	Fetal Heart	heart
8	chr1:223979200-224002200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:223979400-224002600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:223979600-224002400	Strong transcription	Dnd41	blood
11	chr1:223981800-224002600	Weak transcription	Stomach Mucosa	stomach
12	chr1:223982800-224002200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:223984200-224003000	Strong transcription	K562	blood
14	chr1:223985400-224004000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:223988200-224012000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:223990600-224007000	Weak transcription	Fetal Brain Male	brain
17	chr1:223991000-224004400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:223991200-224007400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:223991200-224007400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:223991200-224010800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:223991400-224007600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:223993400-224008400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:223994600-224007000	Weak transcription	Colonic Mucosa	Colon
24	chr1:223994600-224008200	Weak transcription	Psoas Muscle	Psoas
25	chr1:223995600-224002600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:223995800-224009400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:223996000-224007600	Weak transcription	Hela-S3	cervix
28	chr1:223996200-224002600	Weak transcription	A549	lung
29	chr1:223996400-224002200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:223997000-224001400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:223997200-224004600	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:223997600-224002000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:223997600-224002000	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr1:223997800-224002800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:223998000-224002000	Strong transcription	Liver	Liver
36	chr1:223998600-224003200	Weak transcription	HMEC	breast
37	chr1:223999000-224002200	Strong transcription	Placenta	Placenta
38	chr1:223999000-224003200	Weak transcription	NHDF-Ad	bronchial
39	chr1:223999200-224004000	Strong transcription	Fetal Lung	lung
40	chr1:223999400-224002200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:223999400-224004000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:223999600-224001400	Weak transcription	Brain Substantia Nigra	brain
43	chr1:223999600-224002000	Strong transcription	Primary hematopoietic stem cells	blood
44	chr1:223999600-224002400	Strong transcription	Osteobl	bone
45	chr1:223999600-224007800	Weak transcription	Brain Angular Gyrus	brain
46	chr1:223999800-224001400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:223999800-224001400	Strong transcription	Brain Germinal Matrix	brain
48	chr1:223999800-224001800	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr1:223999800-224001800	Strong transcription	Right Ventricle	heart
50	chr1:223999800-224002000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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