Variant report

Variant	rs659025
Chromosome Location	chr6:4119051-4119052
allele	A/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	chr6:4119021-4119146	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:4118884-4119073	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:4118605-4119483	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4112632..4117025-chr6:4117179..4121716,5	K562	blood:

Variant related genes	Relation type
C6orf201	TF binding region

Extended variants
information (count: 103 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs101418	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs11755877	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs1204951	0.92[ASN][1000 genomes]
rs2326408	1.00[ASN][1000 genomes]
rs2473597	0.84[ASN][1000 genomes]
rs2745453	0.84[ASN][1000 genomes]
rs2745455	0.89[ASN][1000 genomes]
rs2783063	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2783073	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28878015	0.91[ASN][1000 genomes]
rs4959271	0.89[ASN][1000 genomes]
rs582008	0.84[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs583782	0.84[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs583881	0.84[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs584585	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs590675	0.84[ASN][1000 genomes]
rs592953	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs593291	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs594662	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs595413	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs608195	1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs609946	0.84[ASN][1000 genomes]
rs611500	1.00[ASN][1000 genomes]
rs612022	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612477	0.93[ASN][1000 genomes]
rs613028	0.97[ASN][1000 genomes]
rs613260	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613709	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617604	0.90[ASN][1000 genomes]
rs617790	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619439	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs619483	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs619873	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620484	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620901	0.83[ASN][1000 genomes]
rs621205	0.90[ASN][1000 genomes]
rs626080	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs627259	0.93[ASN][1000 genomes]
rs629362	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634114	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs634698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634970	0.84[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs638329	0.84[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs639905	1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs643232	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646385	0.84[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs648900	1.00[ASN][1000 genomes]
rs649725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650183	0.81[CHB][hapmap]
rs651246	0.84[ASN][1000 genomes]
rs653431	0.84[ASN][1000 genomes]
rs654621	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs654982	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs659051	0.91[ASN][1000 genomes]
rs659305	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6597031	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs660560	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660957	0.91[ASN][1000 genomes]
rs661404	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs661657	0.92[ASN][1000 genomes]
rs662834	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs664299	0.98[ASN][1000 genomes]
rs664635	0.84[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs664839	0.82[ASN][1000 genomes]
rs664898	0.91[ASN][1000 genomes]
rs665728	1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs665894	0.89[ASN][1000 genomes]
rs666254	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs668070	0.88[ASN][1000 genomes]
rs670932	0.84[ASN][1000 genomes]
rs671364	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs674543	0.89[ASN][1000 genomes]
rs676683	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678285	0.84[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs679303	0.84[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs682063	0.81[CHB][hapmap]
rs688176	1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs689308	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694058	0.91[ASN][1000 genomes]
rs694903	0.93[ASN][1000 genomes]
rs707991	1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7166	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744628	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756630	0.80[ASN][1000 genomes]
rs7757606	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853417	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853418	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9328220	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378395	0.83[ASN][1000 genomes]
rs9405219	0.90[ASN][1000 genomes]
rs9405701	0.91[ASN][1000 genomes]
rs942475	1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs9503919	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs9503922	0.86[ASW][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs9503936	0.84[GIH][hapmap];0.82[TSI][hapmap]

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	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
5	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs659025	PECI	cis	parietal	SCAN
rs659025	ECI2	cis	Thyroid	GTEx
rs659025	PECI	cis	cerebellum	SCAN
rs659025	C6orf201	Cis_1M	lymphoblastoid	RTeQTL
rs659025	PECI	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4110400-4124400	Weak transcription	Fetal Heart	heart
2	chr6:4111000-4134200	Weak transcription	Stomach Mucosa	stomach
3	chr6:4113600-4122200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:4113800-4134600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:4114000-4131400	Strong transcription	Brain Anterior Caudate	brain
6	chr6:4114200-4126200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:4114200-4132200	Strong transcription	Primary T cells from cord blood	blood
8	chr6:4114200-4132800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:4114200-4133400	Strong transcription	Stomach Smooth Muscle	stomach
10	chr6:4114400-4130200	Strong transcription	Liver	Liver
11	chr6:4114400-4131800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:4114400-4132400	Strong transcription	Fetal Thymus	thymus
13	chr6:4114600-4125800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:4114600-4126200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:4114600-4130000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:4114600-4130600	Strong transcription	Brain Germinal Matrix	brain
17	chr6:4114600-4133600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:4114800-4121200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr6:4114800-4121400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:4114800-4122400	Strong transcription	Primary B cells from cord blood	blood
21	chr6:4114800-4123200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:4114800-4125600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:4114800-4132800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr6:4114800-4133400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr6:4115000-4121200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:4115000-4121200	Strong transcription	Fetal Muscle Leg	muscle
27	chr6:4115000-4122400	Strong transcription	Dnd41	blood
28	chr6:4115000-4125400	Strong transcription	NH-A	brain
29	chr6:4115200-4121000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:4115200-4123400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:4115200-4125800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:4115200-4125800	Strong transcription	Adipose Nuclei	Adipose
33	chr6:4115200-4128600	Strong transcription	Brain Hippocampus Middle	brain
34	chr6:4115200-4129800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:4115200-4131200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr6:4115200-4131200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:4115200-4132000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr6:4115200-4132000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:4115200-4132600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:4115200-4132800	Strong transcription	Left Ventricle	heart
41	chr6:4115200-4133000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr6:4115200-4133800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:4115400-4121200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:4115400-4123000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:4115400-4123000	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr6:4115400-4123200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:4115400-4123200	Strong transcription	Brain Substantia Nigra	brain
48	chr6:4115400-4124600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:4115400-4125000	Strong transcription	Osteobl	bone
50	chr6:4115400-4125400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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