Variant report

Variant	rs853411
Chromosome Location	chr6:4063681-4063682
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4038415..4040524-chr6:4062857..4065779,3	K562	blood:
2	chr6:4063481..4065487-chr6:4065794..4068948,3	K562	blood:
3	chr6:4050182..4052432-chr6:4060847..4064150,3	K562	blood:
4	chr6:4049234..4051295-chr6:4063224..4065209,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145975	Chromatin interaction
ENSG00000112739	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs12174184	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12198921	0.80[GIH][hapmap]
rs1408457	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1543355	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]
rs2181894	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2745451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2745452	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs3747761	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3747762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3747763	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3761787	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4466281	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4959916	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4959918	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959919	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6900476	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6905475	0.95[ASN][1000 genomes]
rs6906467	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6910519	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6914180	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6916982	0.83[ASN][1000 genomes]
rs6921738	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6924389	0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6930892	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6933593	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6939049	1.00[JPT][hapmap]
rs6941706	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs697745	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs707980	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs707981	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs707982	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs707983	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs707984	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs707985	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs707987	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs707988	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73349780	0.95[ASN][1000 genomes]
rs7744603	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7763233	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs853396	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs853397	0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs853398	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs853399	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853400	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853402	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs853403	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853404	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853405	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853406	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853407	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853408	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853409	0.82[ASN][1000 genomes]
rs853410	0.85[ASN][1000 genomes]
rs860477	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs860478	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9328215	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9328216	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9405217	0.81[CEU][hapmap]
rs9405693	0.87[CEU][hapmap]
rs9405694	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs941443	0.83[ASN][1000 genomes]
rs942474	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9503893	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs853411	PECI	cis	parietal	SCAN
rs853411	PECI	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4023200-4064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
3	chr6:4023800-4067000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:4030600-4065800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:4030800-4066600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:4031000-4066400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:4031200-4066600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr6:4034000-4066800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:4035600-4064200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr6:4035800-4064600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr6:4035800-4065000	Strong transcription	Dnd41	blood
12	chr6:4035800-4066000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr6:4035800-4066000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr6:4035800-4066200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:4036000-4066600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:4036000-4066600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr6:4037200-4066200	Strong transcription	Liver	Liver
18	chr6:4037400-4065800	Strong transcription	Placenta	Placenta
19	chr6:4037600-4066200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr6:4037600-4066400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr6:4038800-4066000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:4040800-4065400	Strong transcription	GM12878-XiMat	blood
23	chr6:4042000-4066400	Strong transcription	Adipose Nuclei	Adipose
24	chr6:4048200-4064000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:4048200-4064600	Strong transcription	Fetal Intestine Large	intestine
26	chr6:4048200-4065800	Strong transcription	Fetal Muscle Leg	muscle
27	chr6:4048600-4063800	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr6:4052000-4067000	Strong transcription	Primary B cells from cord blood	blood
29	chr6:4052400-4067400	Weak transcription	Psoas Muscle	Psoas
30	chr6:4056000-4065600	Strong transcription	Fetal Kidney	kidney
31	chr6:4056200-4066600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr6:4056400-4064200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr6:4056400-4066400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:4056600-4064000	Strong transcription	Brain Anterior Caudate	brain
35	chr6:4056600-4064200	Strong transcription	Rectal Smooth Muscle	rectum
36	chr6:4056600-4064600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:4056600-4065200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:4056600-4065800	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:4056600-4066200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:4056600-4066800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:4056800-4065200	Strong transcription	Brain Substantia Nigra	brain
42	chr6:4058200-4075000	Weak transcription	Small Intestine	intestine
43	chr6:4058400-4065600	Weak transcription	Gastric	stomach
44	chr6:4059000-4066400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr6:4059200-4063800	Strong transcription	Colon Smooth Muscle	Colon
46	chr6:4059200-4064200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:4059800-4065800	Strong transcription	K562	blood
48	chr6:4059800-4066200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:4059800-4066200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:4059800-4066200	Strong transcription	Hela-S3	cervix

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