Variant report

Variant	rs3095239
Chromosome Location	chr6:31126790-31126791
allele	C/T
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	MAX	chr6:31125928-31126803	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:31126187-31126861	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:31125539-31127594	HepG2	liver:	n/a	n/a
4	NFYB	chr6:31125939-31126832	Hela-S3	cervix:	n/a	chr6:31126259-31126269 chr6:31126254-31126269 chr6:31126257-31126272 chr6:31126257-31126271 chr6:31126257-31126272
5	POLR2A	chr6:31126199-31126844	Hela-S3	cervix:	n/a	n/a
6	ZNF263	chr6:31125975-31126926	HEK293-T-REx	kidney:	n/a	chr6:31126064-31126073 chr6:31126065-31126086 chr6:31126854-31126863
7	MAZ	chr6:31125452-31126914	IMR90	lung:	n/a	n/a
8	POLR2A	chr6:31125636-31127732	GM12892	blood:	n/a	n/a
9	SIN3AK20	chr6:31126051-31126860	PANC-1	pancreas:	n/a	n/a
10	SIN3AK20	chr6:31125759-31127177	MCF-7	breast:	n/a	n/a
11	POLR2A	chr6:31125590-31126790	SK-N-MC	brain:	n/a	n/a
12	MXI1	chr6:31125621-31127412	SK-N-SH	brain:	n/a	n/a
13	SIN3AK20	chr6:31125836-31126894	K562	blood:	n/a	n/a
14	MAX	chr6:31125789-31126977	MCF-7	breast:	n/a	n/a
15	POLR2A	chr6:31125783-31126933	Gliobla	brain:	n/a	n/a
16	ELF1	chr6:31125907-31126815	MCF-7	breast:	n/a	chr6:31126348-31126360 chr6:31125993-31126005 chr6:31125999-31126011
17	HCFC1	chr6:31125138-31126915	Hela-S3	cervix:	n/a	n/a
18	TAF1	chr6:31126219-31126889	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:31125756-31126865	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:31126234-31126812	GM12891	blood:	n/a	n/a
21	RUNX3	chr6:31125713-31127561	GM12878	blood:	n/a	chr6:31127116-31127131 chr6:31127116-31127133
22	NFYB	chr6:31125910-31126791	GM12878	blood:	n/a	chr6:31126259-31126269 chr6:31126254-31126269 chr6:31126257-31126272 chr6:31126257-31126271 chr6:31126257-31126272
23	POLR2A	chr6:31126559-31127652	A549	lung:	n/a	n/a
24	MXI1	chr6:31125636-31127074	IMR90	lung:	n/a	n/a
25	MXI1	chr6:31125915-31126953	GM12878	blood:	n/a	n/a
26	MTA3	chr6:31126058-31128087	GM12878	blood:	n/a	n/a
27	MXI1	chr6:31125903-31126964	Hela-S3	cervix:	n/a	n/a
28	SIN3AK20	chr6:31126133-31126904	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr6:31125655-31128143	H1-hESC	embryonic stem cell:	n/a	n/a
30	ELF1	chr6:31125971-31126823	K562	blood:	n/a	chr6:31126348-31126360 chr6:31125993-31126005 chr6:31125999-31126011
31	SIN3A	chr6:31126147-31127242	GM12878	blood:	n/a	chr6:31126334-31126347
32	TBP	chr6:31126603-31126912	Hela-S3	cervix:	n/a	n/a
33	CEBPB	chr6:31125929-31126808	Hela-S3	cervix:	n/a	n/a
34	RUNX3	chr6:31126480-31127474	GM12878	blood:	n/a	chr6:31127116-31127131 chr6:31127116-31127133
35	POLR2A	chr6:31126717-31127953	H1-hESC	embryonic stem cell:	n/a	n/a
36	NRF1	chr6:31125847-31126894	SK-N-SH	brain:	n/a	chr6:31126021-31126030 chr6:31126084-31126098 chr6:31126019-31126033 chr6:31126084-31126095 chr6:31126861-31126870 chr6:31126084-31126095 chr6:31126016-31126030 chr6:31126019-31126030 chr6:31126081-31126095
37	E2F4	chr6:31125896-31126828	MCF10A-Er-Src	breast:	n/a	chr6:31126206-31126217 chr6:31126205-31126217 chr6:31126020-31126029 chr6:31126234-31126249 chr6:31125904-31125916 chr6:31126293-31126304 chr6:31126279-31126288 chr6:31126085-31126094
38	GTF2F1	chr6:31125956-31126791	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr6:31125626-31126843	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr6:31125710-31126826	Raji	blood:	n/a	n/a
41	POLR2A	chr6:31126119-31128136	GM12892	blood:	n/a	n/a
42	POLR2A	chr6:31126787-31127016	A549	lung:	n/a	n/a
43	POLR2A	chr6:31126209-31126933	Hela-S3	cervix:	n/a	n/a
44	TEAD4	chr6:31125785-31127391	K562	blood:	n/a	n/a
45	POLR2A	chr6:31126612-31127429	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:31126089-31127396	GM12892	blood:	n/a	n/a
47	PML	chr6:31125593-31127444	GM12878	blood:	n/a	chr6:31126591-31126599
48	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:
6	chr6:31120552..31122855-chr6:31123459..31126942,6	MCF-7	breast:

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

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1061118	0.80[ASN][1000 genomes]
rs1419880	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1419881	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2021375	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2073717	0.84[ASN][1000 genomes]
rs2239524	0.84[ASN][1000 genomes]
rs2394882	0.80[ASN][1000 genomes]
rs3094187	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3094193	0.81[ASN][1000 genomes]
rs3094195	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130453	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3130456	0.85[ASN][1000 genomes]
rs3130934	0.81[ASN][1000 genomes]
rs3132526	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3132533	0.82[ASN][1000 genomes]
rs743401	0.85[ASN][1000 genomes]
rs9263787	0.85[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3095239	TCF19	cis	lymphoblastoid	seeQTL
rs3095239	CCHCR1	cis	lymphoblastoid	seeQTL
rs3095239	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL
rs3095239	TCF19	cis	multi-tissue	Pritchard
rs3095239	CCHCR1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31124800-31126800	Active TSS	NHLF	lung
2	chr6:31125000-31127000	Active TSS	Muscle Satellite Cultured Cells	--
3	chr6:31125000-31127400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:31125000-31127800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:31125200-31126800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:31125200-31127400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:31125200-31127800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:31125400-31126800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:31125400-31126800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:31125400-31126800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:31125400-31126800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:31125400-31126800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:31125400-31126800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:31125400-31126800	Active TSS	Brain Hippocampus Middle	brain
15	chr6:31125400-31126800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:31125400-31126800	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr6:31125400-31126800	Active TSS	Fetal Lung	lung
18	chr6:31125400-31126800	Active TSS	Left Ventricle	heart
19	chr6:31125400-31126800	Active TSS	Ovary	ovary
20	chr6:31125400-31126800	Active TSS	Psoas Muscle	Psoas
21	chr6:31125400-31126800	Active TSS	Rectal Smooth Muscle	rectum
22	chr6:31125400-31126800	Active TSS	K562	blood
23	chr6:31125400-31126800	Active TSS	Osteobl	bone
24	chr6:31125400-31127000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:31125400-31127000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:31125400-31127000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:31125400-31127000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:31125400-31127000	Active TSS	Esophagus	oesophagus
29	chr6:31125400-31127000	Active TSS	A549	lung
30	chr6:31125400-31127000	Active TSS	HMEC	breast
31	chr6:31125400-31127000	Active TSS	HSMMtube	muscle
32	chr6:31125400-31127200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:31125400-31127200	Active TSS	Colon Smooth Muscle	Colon
34	chr6:31125400-31127400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:31125400-31127400	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr6:31125400-31127400	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr6:31125400-31127400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:31125400-31127400	Active TSS	Aorta	Aorta
39	chr6:31125400-31127400	Active TSS	NHDF-Ad	bronchial
40	chr6:31125400-31127600	Active TSS	H9 Cell Line	embryonic stem cell
41	chr6:31125400-31127600	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr6:31125400-31127600	Active TSS	Fetal Kidney	kidney
43	chr6:31125400-31127800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:31125400-31128000	Active TSS	GM12878-XiMat	blood
45	chr6:31125600-31126800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:31125600-31126800	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr6:31125600-31126800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:31125600-31126800	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr6:31125600-31126800	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr6:31125600-31126800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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