Variant report

Variant	rs3177253
Chromosome Location	chr6:4133855-4133856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr6:4133781-4134646	HepG2	liver:	n/a	n/a
2	MXI1	chr6:4133783-4136945	SK-N-SH	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:4056059..4057941-chr6:4133460..4135296,2	K562	blood:
2	chr6:4016355..4024618-chr6:4131840..4138381,21	K562	blood:
3	chr6:4017302..4025509-chr6:4131840..4138381,19	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf201-5	chr6:4131253-4134818	NONHSAT107321

No data

Variant related genes	Relation type
ENSG00000234817	TF binding region
ENSG00000254821	TF binding region
ENSG00000230648	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000272248	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1359321	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17677608	1.00[CHB][hapmap]
rs1815510	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2326403	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34446830	1.00[ASN][1000 genomes]
rs35071107	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45529732	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62394175	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71553907	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9503919	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9503922	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3177253	PECI	cis	parietal	SCAN
rs3177253	PECI	cis	lymphoblastoid	seeQTL
rs3177253	PECI	cis	cerebellum	SCAN
rs3177253	RREB1	cis	parietal	SCAN
rs3177253	C6orf201	Cis_1M	lymphoblastoid	RTeQTL

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	chr6:4127000-4134200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:4127000-4134200	Weak transcription	Aorta	Aorta
5	chr6:4127200-4134200	Weak transcription	HMEC	breast
6	chr6:4129400-4134400	Weak transcription	Lung	lung
7	chr6:4131000-4134200	Weak transcription	HSMMtube	muscle
8	chr6:4131200-4134000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:4131200-4134000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:4131200-4134200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr6:4131200-4134200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:4131200-4134200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:4131200-4134400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:4132400-4134000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:4132400-4134200	Weak transcription	Colonic Mucosa	Colon
16	chr6:4132600-4134000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr6:4132600-4134000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:4132600-4134000	Weak transcription	Fetal Lung	lung
19	chr6:4132600-4134200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr6:4132600-4134200	Weak transcription	Gastric	stomach
21	chr6:4132600-4134200	Weak transcription	Psoas Muscle	Psoas
22	chr6:4132600-4134200	Weak transcription	Small Intestine	intestine
23	chr6:4132600-4134200	Weak transcription	HSMM	muscle
24	chr6:4132600-4134400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:4132600-4134400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:4132600-4134400	Weak transcription	Esophagus	oesophagus
27	chr6:4132600-4134400	Weak transcription	Right Ventricle	heart
28	chr6:4132800-4134000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:4132800-4134000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:4132800-4134000	Weak transcription	Thymus	Thymus
31	chr6:4132800-4134000	Weak transcription	GM12878-XiMat	blood
32	chr6:4132800-4134200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:4132800-4134200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:4132800-4134200	Weak transcription	Primary B cells from cord blood	blood
35	chr6:4132800-4134200	Weak transcription	Fetal Kidney	kidney
36	chr6:4132800-4134200	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:4132800-4134200	Weak transcription	Placenta	Placenta
38	chr6:4132800-4134200	Weak transcription	Left Ventricle	heart
39	chr6:4132800-4134200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:4133000-4134000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:4133000-4134200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:4133000-4134400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr6:4133200-4134000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:4133200-4134000	Transcr. at gene 5' and 3'	K562	blood
45	chr6:4133200-4134000	Weak transcription	NHEK	skin
46	chr6:4133200-4134200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:4133200-4134200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr6:4133200-4134200	Weak transcription	Primary T cells from cord blood	blood
49	chr6:4133200-4134200	Enhancers	Brain Hippocampus Middle	brain
50	chr6:4133200-4134200	Weak transcription	Fetal Thymus	thymus

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