Variant report

Variant	rs6678365
Chromosome Location	chr1:224023734-224023735
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	chr1:224023431..224026214-chr1:224032048..224035063,3	MCF-7	breast:
3	chr1:223995561..223997893-chr1:224022146..224025073,2	K562	blood:

Variant related genes	Relation type
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];0.85[MEX][hapmap]
rs10495215	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10495216	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10495217	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10503144	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];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	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]
rs12060361	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066704	0.85[CEU][hapmap]
rs12069561	0.85[CEU][hapmap]
rs12080250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088254	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs12091841	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222138	0.85[CEU][hapmap]
rs1222141	0.85[CEU][hapmap]
rs12563291	0.84[EUR][1000 genomes]
rs12563477	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12563637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][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];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566817	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.95[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];0.88[LWK][hapmap];1.00[ASN][1000 genomes]
rs16842162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[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];0.86[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];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs17557623	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17597	0.84[EUR][1000 genomes]
rs17598	0.85[CEU][hapmap]
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]
rs3738373	0.85[CEU][hapmap]
rs3738374	0.85[CEU][hapmap]
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]
rs4653522	0.85[CEU][hapmap]
rs4993742	0.82[CEU][hapmap]
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	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]
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]
rs6604729	1.00[AFR][1000 genomes];1.00[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]
rs6671245	1.00[CEU][hapmap]
rs6682964	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683052	1.00[CEU][hapmap]
rs6685475	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6685557	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]
rs6691315	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]
rs6693372	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6693884	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6694960	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]
rs6696053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6696222	1.00[ASN][1000 genomes]
rs6700366	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]
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];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[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	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530328	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]
rs7533551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535882	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[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:122 , 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	chr1:224014200-224024400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:224015200-224023800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:224015400-224025000	Weak transcription	Fetal Stomach	stomach
9	chr1:224015800-224024200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:224017600-224026800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:224019000-224026400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:224019400-224024800	Enhancers	Brain Hippocampus Middle	brain
13	chr1:224019400-224025400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:224019400-224025600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:224019400-224026400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr1:224019400-224026400	Enhancers	Primary T cells from cord blood	blood
17	chr1:224019400-224027000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr1:224019600-224024600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:224019600-224024600	Enhancers	Brain Cingulate Gyrus	brain
20	chr1:224019600-224027400	Enhancers	Fetal Heart	heart
21	chr1:224019800-224025400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr1:224019800-224026600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr1:224020000-224024800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr1:224020200-224026400	Enhancers	HUVEC	blood vessel
25	chr1:224020400-224025800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:224020600-224023800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:224020600-224023800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:224020600-224024000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:224020600-224024400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:224020600-224024400	Weak transcription	HSMMtube	muscle
31	chr1:224020600-224025000	Weak transcription	Brain Germinal Matrix	brain
32	chr1:224020600-224032400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:224020800-224023800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:224020800-224023800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:224020800-224023800	Weak transcription	Esophagus	oesophagus
36	chr1:224020800-224023800	Weak transcription	Lung	lung
37	chr1:224020800-224023800	Weak transcription	Right Ventricle	heart
38	chr1:224020800-224024400	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:224020800-224025000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:224020800-224028600	Weak transcription	Placenta	Placenta
41	chr1:224020800-224031600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:224021200-224027000	Enhancers	Brain Substantia Nigra	brain
43	chr1:224021400-224024600	Enhancers	Gastric	stomach
44	chr1:224021400-224026000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:224021400-224026000	Enhancers	Duodenum Mucosa	Duodenum
46	chr1:224021400-224027000	Enhancers	Fetal Lung	lung
47	chr1:224021600-224025600	Enhancers	Colon Smooth Muscle	Colon
48	chr1:224021800-224024000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:224021800-224024000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr1:224021800-224024400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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