Variant report

Variant	rs6700366
Chromosome Location	chr1:224013080-224013081
allele	C/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	POLR2A	chr1:224013074-224014189	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:224011037..224013548-chr1:224029939..224032384,3	MCF-7	breast:
2	chr1:224010948..224013248-chr1:224034252..224035836,2	MCF-7	breast:
3	chr1:224011114..224014049-chr1:224032766..224036091,4	MCF-7	breast:

Variant related genes	Relation type
TP53BP2	TF binding region
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10465524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs10495215	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10495216	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs10495217	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs10503144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.91[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	0.90[EUR][1000 genomes]
rs12059128	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059770	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]
rs12060361	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066704	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs12069561	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs12080250	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088254	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12091841	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222138	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs1222141	0.85[CEU][hapmap]
rs12563291	0.84[EUR][1000 genomes]
rs12563477	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12563637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];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[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]
rs12566817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[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];0.83[LWK][hapmap];1.00[ASN][1000 genomes]
rs16842162	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842229	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16842257	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[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];0.91[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];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs17557623	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17597	0.84[EUR][1000 genomes]
rs17598	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs28370069	0.83[EUR][1000 genomes]
rs28370073	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28370074	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28370088	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28370159	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370170	0.91[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	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738373	0.85[CEU][hapmap]
rs3738374	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs3767716	0.81[EUR][1000 genomes]
rs3885657	0.95[AMR][1000 genomes];0.96[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]
rs61823580	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61823581	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823583	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823585	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823587	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823591	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824003	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824005	0.94[EUR][1000 genomes]
rs61824008	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604724	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]
rs6604727	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604728	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604729	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604730	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658954	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665485	0.81[EUR][1000 genomes]
rs6671245	1.00[CEU][hapmap]
rs6678365	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682964	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683052	1.00[CEU][hapmap]
rs6685475	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6685557	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]
rs6691315	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]
rs6693372	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6693884	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6694960	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]
rs6696053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6696222	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	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515821	1.00[ASN][1000 genomes]
rs751609	0.85[CEU][hapmap]
rs7528455	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530328	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]
rs7533551	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]
rs7535882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549063	1.00[CEU][hapmap];1.00[JPT][hapmap]

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:118 , 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	chr1:224002000-224015000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:224002000-224023800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:224002200-224020200	Weak transcription	Placenta	Placenta
5	chr1:224002200-224020200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:224002400-224013600	Weak transcription	Esophagus	oesophagus
7	chr1:224003400-224013200	Weak transcription	HepG2	liver
8	chr1:224003800-224013600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:224003800-224014800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:224004200-224014800	Weak transcription	HMEC	breast
11	chr1:224007000-224024000	Weak transcription	Fetal Intestine Small	intestine
12	chr1:224007400-224015200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:224007800-224013400	Weak transcription	Ovary	ovary
14	chr1:224007800-224020200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:224008000-224017000	Weak transcription	Fetal Kidney	kidney
16	chr1:224008000-224019800	Weak transcription	Brain Germinal Matrix	brain
17	chr1:224008200-224019400	Weak transcription	Hela-S3	cervix
18	chr1:224008600-224013400	Weak transcription	Adipose Nuclei	Adipose
19	chr1:224008600-224015000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:224008600-224019400	Weak transcription	A549	lung
21	chr1:224008800-224013600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:224008800-224020200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:224009000-224013400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:224009000-224013400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:224009000-224014800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:224009000-224014800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:224009000-224018800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:224009000-224019400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:224009000-224019400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:224009000-224020400	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:224009200-224013200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:224009200-224013400	Weak transcription	Thymus	Thymus
33	chr1:224009200-224013600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:224009200-224013600	Weak transcription	Brain Anterior Caudate	brain
35	chr1:224009200-224013600	Weak transcription	Dnd41	blood
36	chr1:224009200-224013800	Weak transcription	Aorta	Aorta
37	chr1:224009200-224014800	Weak transcription	NHEK	skin
38	chr1:224009200-224015000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:224009200-224019600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:224009200-224020400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:224009400-224013200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:224009400-224013200	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:224009400-224013400	Weak transcription	Brain Substantia Nigra	brain
44	chr1:224009400-224013600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:224009400-224014600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:224009400-224014800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:224009400-224014800	Weak transcription	Fetal Stomach	stomach
48	chr1:224009400-224015000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:224009400-224019400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:224009400-224019800	Weak transcription	HSMM	muscle

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