Variant report

Variant	rs11751668
Chromosome Location	chr6:4125474-4125475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr6:4050000..4052650-chr6:4123056..4125495,2	K562	blood:
5	chr6:4119267..4120773-chr6:4124628..4126878,2	K562	blood:

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

Variant related genes	Relation type
ENSG00000145975	Chromatin interaction
ENSG00000198721	Chromatin interaction
ENSG00000230648	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000234817	Chromatin interaction
ENSG00000272248	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11753305	0.81[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs11754487	0.86[ASN][1000 genomes]
rs11754986	0.99[ASN][1000 genomes]
rs3789215	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3804317	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3812186	0.96[ASN][1000 genomes]
rs4443542	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583782	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs583881	1.00[ASW][hapmap];0.82[CEU][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs634970	0.82[CEU][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs646385	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs659051	0.83[EUR][1000 genomes]
rs6597031	0.82[JPT][hapmap]
rs660957	0.83[EUR][1000 genomes]
rs664635	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs664898	0.83[EUR][1000 genomes]
rs678285	1.00[ASW][hapmap];0.82[CEU][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs679303	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6916172	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[ASN][1000 genomes]
rs6932036	0.85[ASN][1000 genomes]
rs6935587	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs694058	0.83[EUR][1000 genomes]
rs7166	0.87[JPT][hapmap]
rs853418	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs9378841	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs9378842	1.00[ASN][1000 genomes]
rs9378843	0.85[ASN][1000 genomes]
rs9392552	1.00[ASN][1000 genomes]
rs9392554	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs9392555	0.97[ASN][1000 genomes]
rs9392556	0.81[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs9392560	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs9405220	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs9405221	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs9405684	1.00[YRI][hapmap]
rs9405685	1.00[YRI][hapmap]
rs9405701	0.83[EUR][1000 genomes]
rs9405702	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs9503933	0.98[ASN][1000 genomes]
rs9503934	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs9503936	0.87[JPT][hapmap];0.86[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11751668	PECI	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4111000-4134200	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	chr6:4114600-4125800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:4114600-4126200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:4114600-4130000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:4114600-4130600	Strong transcription	Brain Germinal Matrix	brain
15	chr6:4114600-4133600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:4114800-4125600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:4114800-4132800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr6:4114800-4133400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr6:4115200-4125800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:4115200-4125800	Strong transcription	Adipose Nuclei	Adipose
21	chr6:4115200-4128600	Strong transcription	Brain Hippocampus Middle	brain
22	chr6:4115200-4129800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:4115200-4131200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr6:4115200-4131200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:4115200-4132000	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr6:4115200-4132000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:4115200-4132600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr6:4115200-4132800	Strong transcription	Left Ventricle	heart
29	chr6:4115200-4133000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr6:4115200-4133800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:4115400-4129000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:4115400-4131000	Strong transcription	Fetal Brain Female	brain
33	chr6:4115400-4131200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr6:4115400-4131400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:4115400-4133200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:4115400-4133400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:4115400-4133800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr6:4115600-4125600	Strong transcription	HepG2	liver
39	chr6:4115600-4125800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:4115600-4126400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:4115600-4129000	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:4115600-4129400	Strong transcription	Brain Angular Gyrus	brain
43	chr6:4115600-4131000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr6:4115600-4131000	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr6:4115600-4131200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:4115600-4131400	Strong transcription	Fetal Lung	lung
47	chr6:4115600-4132200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:4115600-4132200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:4115600-4132600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr6:4116200-4127400	Weak transcription	GM12878-XiMat	blood

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