Variant report

Variant	rs660560
Chromosome Location	chr6:4125941-4125942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:4018891..4022947-chr6:4124925..4128719,4	K562	blood:
2	chr6:4124643..4126417-chr6:4135807..4137737,2	MCF-7	breast:
3	chr6:4112263..4113921-chr6:4124338..4126285,2	K562	blood:
4	chr6:4119267..4120773-chr6:4124628..4126878,2	K562	blood:
5	chr6:4125770..4127713-chr6:4129299..4130980,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf201-4	chr6:4125213-4126353	NR_104464
2	lnc-C6orf201-4	chr6:4125589-4129180	NONHSAT107320

No data

Variant related genes	Relation type
ENSG00000234817	Chromatin interaction
ENSG00000272248	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000198721	Chromatin interaction
ENSG00000230648	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs101418	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs11755877	0.95[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	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2783073	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28878015	0.91[ASN][1000 genomes]
rs4959271	0.89[ASN][1000 genomes]
rs582008	0.85[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs583782	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs583881	0.85[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs584585	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590675	0.84[ASN][1000 genomes]
rs592953	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs593291	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs594662	0.95[CHB][hapmap];0.80[CHD][hapmap];0.84[ASN][1000 genomes]
rs595413	0.95[CHB][hapmap];0.80[CHD][hapmap];0.84[ASN][1000 genomes]
rs608195	0.95[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];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612477	0.93[ASN][1000 genomes]
rs613028	0.97[ASN][1000 genomes]
rs613260	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613709	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617604	0.90[ASN][1000 genomes]
rs617790	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[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619439	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs619483	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs619873	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620484	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[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];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs627259	0.93[ASN][1000 genomes]
rs629362	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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633290	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634114	0.95[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];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634970	0.85[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs638329	0.85[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs639905	0.95[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs643232	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651246	0.84[ASN][1000 genomes]
rs653431	0.84[ASN][1000 genomes]
rs654621	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs654982	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs659025	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]
rs659051	0.91[ASN][1000 genomes]
rs659305	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6597031	0.95[CEU][hapmap];0.93[EUR][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	0.95[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	0.93[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs665894	0.89[ASN][1000 genomes]
rs666254	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs668070	0.88[ASN][1000 genomes]
rs670932	0.84[ASN][1000 genomes]
rs671364	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs674543	0.89[ASN][1000 genomes]
rs676683	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678285	0.85[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs679303	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs688176	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs689308	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694058	0.91[ASN][1000 genomes]
rs694903	0.93[ASN][1000 genomes]
rs707991	0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7166	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[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];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756630	0.80[ASN][1000 genomes]
rs7757606	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853416	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853417	0.94[AMR][1000 genomes];0.99[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];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[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	0.95[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][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
rs660560	PECI	cis	cerebellum	SCAN
rs660560	PECI	cis	lymphoblastoid	seeQTL
rs660560	C6orf201	Cis_1M	lymphoblastoid	RTeQTL
rs660560	ECI2	cis	Thyroid	GTEx
rs660560	PECI	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4111000-4134200	Weak transcription	Stomach Mucosa	stomach
2	chr6:4113800-4134600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:4114000-4131400	Strong transcription	Brain Anterior Caudate	brain
4	chr6:4114200-4126200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:4114200-4132200	Strong transcription	Primary T cells from cord blood	blood
6	chr6:4114200-4132800	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:4114200-4133400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr6:4114400-4130200	Strong transcription	Liver	Liver
9	chr6:4114400-4131800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:4114400-4132400	Strong transcription	Fetal Thymus	thymus
11	chr6:4114600-4126200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:4114600-4130000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:4114600-4130600	Strong transcription	Brain Germinal Matrix	brain
14	chr6:4114600-4133600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:4114800-4132800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr6:4114800-4133400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr6:4115200-4128600	Strong transcription	Brain Hippocampus Middle	brain
18	chr6:4115200-4129800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:4115200-4131200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr6:4115200-4131200	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:4115200-4132000	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr6:4115200-4132000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:4115200-4132600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:4115200-4132800	Strong transcription	Left Ventricle	heart
25	chr6:4115200-4133000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr6:4115200-4133800	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:4115400-4129000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:4115400-4131000	Strong transcription	Fetal Brain Female	brain
29	chr6:4115400-4131200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr6:4115400-4131400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:4115400-4133200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:4115400-4133400	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:4115400-4133800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr6:4115600-4126400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:4115600-4129000	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:4115600-4129400	Strong transcription	Brain Angular Gyrus	brain
37	chr6:4115600-4131000	Strong transcription	Brain Cingulate Gyrus	brain
38	chr6:4115600-4131000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr6:4115600-4131200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:4115600-4131400	Strong transcription	Fetal Lung	lung
41	chr6:4115600-4132200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:4115600-4132200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:4115600-4132600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr6:4116200-4127400	Weak transcription	GM12878-XiMat	blood
45	chr6:4116200-4132000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:4117400-4126600	Weak transcription	Right Atrium	heart
47	chr6:4119400-4128200	Weak transcription	Psoas Muscle	Psoas
48	chr6:4121200-4132000	Strong transcription	Primary hematopoietic stem cells	blood
49	chr6:4121600-4130400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:4121600-4132200	Strong transcription	HUES6 Cell Line	embryonic stem cell

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