Variant report

Variant	rs1543355
Chromosome Location	chr6:4065753-4065754
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4061684..4064078-chr6:4064643..4066598,2	MCF-7	breast:
2	chr6:4064462..4067328-chr6:4134319..4137285,4	K562	blood:
3	chr6:4061052..4063122-chr6:4065712..4067920,2	K562	blood:
4	chr6:4038415..4040524-chr6:4062857..4065779,3	K562	blood:
5	chr6:4064462..4068135-chr6:4134400..4138606,5	K562	blood:
6	chr6:4063923..4066758-chr6:4130890..4132765,2	K562	blood:
7	chr6:4063965..4066148-chr6:4066336..4068654,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234817	Chromatin interaction
ENSG00000254821	Chromatin interaction
ENSG00000198721	Chromatin interaction
ENSG00000112739	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12174184	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1408457	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2181894	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2745451	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2745452	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs3747761	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3747762	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3747763	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3761787	0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4466281	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4959916	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4959918	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4959919	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6900476	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6905475	0.91[ASN][1000 genomes]
rs6906467	0.91[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6910519	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6914180	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6916982	0.81[ASN][1000 genomes]
rs6921738	0.80[EUR][1000 genomes]
rs6924389	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6930892	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6933593	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6939049	1.00[JPT][hapmap]
rs6941706	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs697745	0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs707980	0.91[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs707981	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs707982	0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs707983	0.91[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs707984	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs707985	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs707987	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs707988	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73349780	0.99[ASN][1000 genomes]
rs7744603	0.85[ASN][1000 genomes]
rs7763233	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs853396	0.91[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853397	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs853398	0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs853399	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs853400	0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs853402	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs853403	0.91[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853404	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853405	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853406	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853407	0.91[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853408	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853410	0.81[ASN][1000 genomes]
rs853411	0.95[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs860477	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs860478	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9328215	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9328216	0.91[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9405217	0.84[CEU][hapmap]
rs9405693	0.91[CEU][hapmap]
rs9405694	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs941443	0.81[ASN][1000 genomes]
rs942474	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9503893	0.91[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv462615	chr6:4052383-4096678	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv600860	chr6:4052383-4096678	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 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	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
2	chr6:4023800-4067000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:4030600-4065800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:4030800-4066600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:4031000-4066400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:4031200-4066600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr6:4034000-4066800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:4035800-4066000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr6:4035800-4066000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr6:4035800-4066200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:4036000-4066600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:4036000-4066600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr6:4037200-4066200	Strong transcription	Liver	Liver
14	chr6:4037400-4065800	Strong transcription	Placenta	Placenta
15	chr6:4037600-4066200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr6:4037600-4066400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:4038800-4066000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:4042000-4066400	Strong transcription	Adipose Nuclei	Adipose
19	chr6:4048200-4065800	Strong transcription	Fetal Muscle Leg	muscle
20	chr6:4052000-4067000	Strong transcription	Primary B cells from cord blood	blood
21	chr6:4052400-4067400	Weak transcription	Psoas Muscle	Psoas
22	chr6:4056200-4066600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:4056400-4066400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:4056600-4065800	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:4056600-4066200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:4056600-4066800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:4058200-4075000	Weak transcription	Small Intestine	intestine
28	chr6:4059000-4066400	Strong transcription	Stomach Smooth Muscle	stomach
29	chr6:4059800-4065800	Strong transcription	K562	blood
30	chr6:4059800-4066200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:4059800-4066200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:4059800-4066200	Strong transcription	Hela-S3	cervix
33	chr6:4060000-4066400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:4060000-4067000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:4060200-4066200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr6:4060200-4066200	Strong transcription	HUVEC	blood vessel
37	chr6:4060200-4066400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:4060200-4067000	Strong transcription	Fetal Thymus	thymus
39	chr6:4060200-4067200	Weak transcription	Fetal Intestine Small	intestine
40	chr6:4060400-4066000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:4060400-4066000	Strong transcription	A549	lung
42	chr6:4060400-4066400	Weak transcription	Pancreas	Pancrea
43	chr6:4060400-4066600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:4060400-4066600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:4060400-4067000	Strong transcription	Primary T cells from cord blood	blood
46	chr6:4060400-4068200	Weak transcription	Ovary	ovary
47	chr6:4060600-4065800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr6:4060600-4065800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:4060600-4066400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:4060600-4066400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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