Variant report

Variant	rs3778173
Chromosome Location	chr6:133137322-133137323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:78)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:78 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:133133973-133142719	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:133136894-133138284	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr6:133135032-133137592	HCT-116	colon:	n/a	n/a
4	POLR2A	chr6:133134162-133138350	GM12892	blood:	n/a	n/a
5	POLR2A	chr6:133133509-133142958	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:133136999-133137974	Hela-S3	cervix:	n/a	n/a
7	MYC	chr6:133133521-133138056	K562	blood:	n/a	chr6:133134081-133134091 chr6:133135767-133135777
8	POLR2A	chr6:133136972-133137338	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:133134007-133138262	GM15510	blood:	n/a	n/a
10	POLR2A	chr6:133134121-133142902	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr6:133135219-133144621	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:133135075-133142824	K562	blood:	n/a	n/a
13	POLR2A	chr6:133134120-133142624	GM18505	blood:	n/a	n/a
14	HEY1	chr6:133136990-133137372	K562	blood:	n/a	n/a
15	POLR2A	chr6:133136987-133137589	ECC-1	luminal epithelium:	n/a	n/a
16	TAF7	chr6:133134418-133138128	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr6:133133442-133144695	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr6:133133522-133142994	GM12891	blood:	n/a	n/a
19	POLR2A	chr6:133135035-133138163	U87	brain:	n/a	n/a
20	POLR2A	chr6:133137306-133137883	GM12891	blood:	n/a	n/a
21	POLR2A	chr6:133133648-133142538	K562	blood:	n/a	n/a
22	POLR2A	chr6:133137026-133138035	K562	blood:	n/a	n/a
23	POLR2A	chr6:133136985-133138228	GM12891	blood:	n/a	n/a
24	POLR2A	chr6:133134946-133142915	U87	brain:	n/a	n/a
25	POLR2A	chr6:133134298-133142858	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr6:133133488-133142945	PBDE	blood:	n/a	n/a
27	POLR2A	chr6:133133410-133142612	HepG2	liver:	n/a	n/a
28	POLR2A	chr6:133133546-133143142	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr6:133134132-133137981	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr6:133137037-133138286	GM12891	blood:	n/a	n/a
31	POLR2A	chr6:133136910-133143141	MCF-7	breast:	n/a	n/a
32	POLR2A	chr6:133137198-133138298	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr6:133133915-133137993	GM19099	blood:	n/a	n/a
34	POLR2A	chr6:133133528-133143521	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr6:133133461-133143479	K562	blood:	n/a	n/a
36	POLR2A	chr6:133133600-133142470	K562	blood:	n/a	n/a
37	CEBPB	chr6:133136910-133137668	HepG2	liver:	n/a	n/a
38	POLR2A	chr6:133135013-133142637	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr6:133136821-133141459	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:133137115-133142750	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr6:133137029-133138163	A549	lung:	n/a	n/a
42	CHD1	chr6:133133718-133139140	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr6:133136825-133137323	HUVEC	blood vessel:	n/a	n/a
44	ATF2	chr6:133137238-133138580	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr6:133133566-133142521	K562	blood:	n/a	n/a
46	POLR2A	chr6:133135089-133137705	IMR90	lung:	n/a	n/a
47	POLR2A	chr6:133137301-133138225	GM12891	blood:	n/a	n/a
48	HEY1	chr6:133137025-133141401	HepG2	liver:	n/a	n/a
49	MXI1	chr6:133134007-133137672	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr6:133134688-133138413	PANC-1	pancreas:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52224699..52226307-chr6:133135521..133137429,2	MCF-7	breast:
2	chr6:133054032..133057251-chr6:133136548..133139421,3	K562	blood:
3	chr17:40214097..40215598-chr6:133136759..133139699,2	K562	blood:
4	chr6:133049609..133052376-chr6:133137041..133138744,2	MCF-7	breast:
5	chr6:132855902..132859597-chr6:133135974..133139810,3	K562	blood:
6	chr6:133084415..133087080-chr6:133134762..133137402,2	MCF-7	breast:
7	chr6:133118544..133124606-chr6:133132137..133138834,13	MCF-7	breast:
8	chr6:133135604..133137467-chr6:144606007..144608305,2	K562	blood:
9	chr6:133117688..133126502-chr6:133133829..133139054,19	MCF-7	breast:

No data

Variant related genes	Relation type
SNORA33	TF binding region
SNORD100	TF binding region
ENSG00000146409	Chromatin interaction
ENSG00000152818	Chromatin interaction
ENSG00000237110	Chromatin interaction
ENSG00000235415	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000112303	Chromatin interaction
ENSG00000093134	Chromatin interaction
ENSG00000187595	Chromatin interaction
ENSG00000271488	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10457591	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10457593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457595	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457596	0.85[CEU][hapmap]
rs10484628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11154698	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128998	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11758796	0.81[ASN][1000 genomes]
rs12190684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191058	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193474	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12194625	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12194802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195249	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196336	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197430	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12198970	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12199381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12200848	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201540	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201769	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12202407	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203738	0.92[ASN][1000 genomes]
rs12204027	1.00[CHB][hapmap]
rs12204693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12204863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12209144	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12211425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212934	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12215084	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215088	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12215486	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061751	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143387	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2294761	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28693848	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706652	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813347	1.00[JPT][hapmap]
rs55708537	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959738	0.85[ASN][1000 genomes]
rs56170227	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58265543	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59543333	0.82[EUR][1000 genomes]
rs60062075	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60412119	0.85[ASN][1000 genomes]
rs62425110	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425113	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425114	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425133	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425137	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426668	0.81[ASN][1000 genomes]
rs62426674	0.81[ASN][1000 genomes]
rs6934161	1.00[CHB][hapmap]
rs9375919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389032	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389033	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402452	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402453	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402455	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9493445	1.00[CHB][hapmap]
rs9493446	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv886676	chr6:133111706-133168582	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	esv1806734	chr6:133125643-133168582	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3778173	C6orf192	cis	multi-tissue	Pritchard
rs3778173	C6orf192	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133134000-133137800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:133134000-133138400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:133134600-133138400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:133135800-133137400	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr6:133135800-133137400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:133135800-133138000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
7	chr6:133135800-133138400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
8	chr6:133136000-133137400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
9	chr6:133136000-133137800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:133136000-133138000	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
11	chr6:133136000-133138000	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
12	chr6:133136000-133138000	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
13	chr6:133136000-133138000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
14	chr6:133136000-133138000	Transcr. at gene 5' and 3'	Fetal Lung	lung
15	chr6:133136000-133138000	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
16	chr6:133136000-133138200	Transcr. at gene 5' and 3'	Dnd41	blood
17	chr6:133136000-133138200	Transcr. at gene 5' and 3'	NHEK	skin
18	chr6:133136000-133138200	Transcr. at gene 5' and 3'	Osteobl	bone
19	chr6:133136000-133138400	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
20	chr6:133136000-133138400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
21	chr6:133136000-133138400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:133136000-133138400	Transcr. at gene 5' and 3'	HMEC	breast
23	chr6:133136000-133138600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
24	chr6:133136000-133139000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
25	chr6:133136000-133139200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
26	chr6:133136000-133139200	Transcr. at gene 5' and 3'	K562	blood
27	chr6:133136000-133139800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:133136200-133137400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr6:133136200-133137400	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr6:133136200-133137800	Transcr. at gene 5' and 3'	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:133136200-133137800	Transcr. at gene 5' and 3'	HSMM	muscle
32	chr6:133136200-133138000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:133136200-133138000	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
34	chr6:133136200-133138200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:133136200-133138200	Transcr. at gene 5' and 3'	Hela-S3	cervix
36	chr6:133136200-133138400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:133136200-133138400	Transcr. at gene 5' and 3'	NHLF	lung
38	chr6:133136200-133138600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:133136200-133138600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:133136200-133138600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
41	chr6:133136200-133139000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:133136200-133139000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
43	chr6:133136200-133139400	Transcr. at gene 5' and 3'	A549	lung
44	chr6:133136200-133140600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
45	chr6:133136400-133137400	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr6:133136400-133137400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:133136400-133137400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr6:133136400-133137600	Flanking Active TSS	Fetal Heart	heart
49	chr6:133136400-133137600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
50	chr6:133136400-133138000	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain

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