Variant report

Variant	rs3094187
Chromosome Location	chr6:31126944-31126945
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	chr6:31126923-31127309	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr6:31125539-31127594	HepG2	liver:	n/a	n/a
3	YY1	chr6:31126917-31127463	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:31125636-31127732	GM12892	blood:	n/a	n/a
5	SIN3AK20	chr6:31125759-31127177	MCF-7	breast:	n/a	n/a
6	STAT3	chr6:31126921-31126959	MCF10A-Er-Src	breast:	n/a	n/a
7	MXI1	chr6:31125621-31127412	SK-N-SH	brain:	n/a	n/a
8	MAX	chr6:31125789-31126977	MCF-7	breast:	n/a	n/a
9	RUNX3	chr6:31125713-31127561	GM12878	blood:	n/a	chr6:31127116-31127131 chr6:31127116-31127133
10	CTCF	chr6:31126900-31127050	GM12867	blood:	n/a	n/a
11	POLR2A	chr6:31126559-31127652	A549	lung:	n/a	n/a
12	MXI1	chr6:31125636-31127074	IMR90	lung:	n/a	n/a
13	MXI1	chr6:31125915-31126953	GM12878	blood:	n/a	n/a
14	MTA3	chr6:31126058-31128087	GM12878	blood:	n/a	n/a
15	MXI1	chr6:31125903-31126964	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:31125655-31128143	H1-hESC	embryonic stem cell:	n/a	n/a
17	IKZF1	chr6:31126921-31127239	GM12878	blood:	n/a	n/a
18	SIN3A	chr6:31126147-31127242	GM12878	blood:	n/a	chr6:31126334-31126347
19	POLR2A	chr6:31126926-31127063	H1-hESC	embryonic stem cell:	n/a	n/a
20	NFIC	chr6:31126847-31127354	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:31126935-31126950	Gliobla	brain:	n/a	n/a
22	RUNX3	chr6:31126480-31127474	GM12878	blood:	n/a	chr6:31127116-31127131 chr6:31127116-31127133
23	POLR2A	chr6:31126717-31127953	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr6:31126119-31128136	GM12892	blood:	n/a	n/a
25	POLR2A	chr6:31126787-31127016	A549	lung:	n/a	n/a
26	TEAD4	chr6:31125785-31127391	K562	blood:	n/a	n/a
27	POLR2A	chr6:31126612-31127429	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:31126089-31127396	GM12892	blood:	n/a	n/a
29	POLR2A	chr6:31126875-31127382	PFSK-1	brain:	n/a	n/a
30	PML	chr6:31125593-31127444	GM12878	blood:	n/a	chr6:31126591-31126599
31	SIN3A	chr6:31125657-31127508	H1-hESC	embryonic stem cell:	n/a	chr6:31125892-31125905 chr6:31126334-31126347 chr6:31125894-31125905

No.	Distal block	Cell Line	Cell type
1	chr6:31125954..31128399-chr6:31147370..31149956,2	MCF-7	breast:
2	chr6:31124835..31127745-chr6:31135310..31138711,4	MCF-7	breast:
3	chr6:31119377..31122828-chr6:31124699..31127188,7	K562	blood:
4	chr6:31103871..31105834-chr6:31123155..31127372,3	MCF-7	breast:
5	chr6:31103022..31109591-chr6:31125707..31129394,9	MCF-7	breast:

Variant related genes	Relation type
TCF19	TF binding region
CCHCR1	TF binding region
ENSG00000204531	Chromatin interaction
ENSG00000204536	Chromatin interaction
ENSG00000204538	Chromatin interaction
ENSG00000238211	Chromatin interaction
ENSG00000204540	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1061118	0.81[ASN][1000 genomes]
rs1419880	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1419881	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2021375	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2073717	0.84[ASN][1000 genomes]
rs2239524	0.83[ASN][1000 genomes]
rs2394882	0.81[ASN][1000 genomes]
rs3094193	0.82[ASN][1000 genomes]
rs3094195	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095239	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130453	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130456	0.84[ASN][1000 genomes]
rs3130934	0.80[ASN][1000 genomes]
rs3132526	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3132533	0.81[ASN][1000 genomes]
rs743401	0.84[ASN][1000 genomes]
rs9263787	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
14	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
15	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
16	nsv524061	chr6:31107087-31133943	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv884138	chr6:31114573-31129707	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3094187	TCF19	cis	lymphoblastoid	seeQTL
rs3094187	HLA-C	cis	multi-tissue	Pritchard
rs3094187	HLA-DRB5	cis	multi-tissue	Pritchard
rs3094187	TCF19	cis	multi-tissue	Pritchard
rs3094187	CCHCR1	cis	lymphoblastoid	seeQTL
rs3094187	HCG27	cis	multi-tissue	Pritchard
rs3094187	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL
rs3094187	HLA-DRB1	cis	multi-tissue	Pritchard
rs3094187	CCHCR1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31125000-31127000	Active TSS	Muscle Satellite Cultured Cells	--
2	chr6:31125000-31127400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:31125000-31127800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:31125200-31127400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:31125200-31127800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:31125400-31127000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:31125400-31127000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:31125400-31127000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:31125400-31127000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:31125400-31127000	Active TSS	Esophagus	oesophagus
11	chr6:31125400-31127000	Active TSS	A549	lung
12	chr6:31125400-31127000	Active TSS	HMEC	breast
13	chr6:31125400-31127000	Active TSS	HSMMtube	muscle
14	chr6:31125400-31127200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:31125400-31127200	Active TSS	Colon Smooth Muscle	Colon
16	chr6:31125400-31127400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:31125400-31127400	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr6:31125400-31127400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr6:31125400-31127400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:31125400-31127400	Active TSS	Aorta	Aorta
21	chr6:31125400-31127400	Active TSS	NHDF-Ad	bronchial
22	chr6:31125400-31127600	Active TSS	H9 Cell Line	embryonic stem cell
23	chr6:31125400-31127600	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:31125400-31127600	Active TSS	Fetal Kidney	kidney
25	chr6:31125400-31127800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:31125400-31128000	Active TSS	GM12878-XiMat	blood
27	chr6:31125600-31127000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:31125600-31127000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:31125600-31127000	Active TSS	Placenta Amnion	Placenta Amnion
30	chr6:31125600-31127000	Active TSS	Dnd41	blood
31	chr6:31125600-31127000	Active TSS	Hela-S3	cervix
32	chr6:31125600-31127200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr6:31125600-31127200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:31125600-31127200	Active TSS	Small Intestine	intestine
35	chr6:31125600-31127200	Active TSS	Thymus	Thymus
36	chr6:31125600-31127600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:31125600-31127800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr6:31125800-31127000	Active TSS	NH-A	brain
39	chr6:31126200-31127600	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr6:31126400-31127000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr6:31126400-31127000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr6:31126400-31127000	Flanking Active TSS	Liver	Liver
43	chr6:31126400-31127000	Active TSS	Right Atrium	heart
44	chr6:31126400-31127200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr6:31126400-31127200	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr6:31126400-31127200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr6:31126400-31127200	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr6:31126400-31127200	Flanking Active TSS	Placenta	Placenta
49	chr6:31126400-31127200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr6:31126400-31127200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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