Variant report

Variant	rs3095300
Chromosome Location	chr6:31082476-31082477
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	SMARCC1	chr6:31081841-31083341	Hela-S3	cervix:	n/a	chr6:31082449-31082458
2	POLR2A	chr6:31082044-31082957	PFSK-1	brain:	n/a	n/a
3	FOSL2	chr6:31082300-31082778	SK-N-SH	brain:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
4	REST	chr6:31082219-31082725	SK-N-SH	brain:	n/a	chr6:31082466-31082479
5	POLR2A	chr6:31082230-31082609	MCF-7	breast:	n/a	n/a
6	MAFK	chr6:31082385-31082576	Hela-S3	cervix:	n/a	n/a
7	FOS	chr6:31082302-31083000	MCF10A-Er-Src	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082458 chr6:31082447-31082459 chr6:31082448-31082458
8	FOSL2	chr6:31082102-31082797	A549	lung:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
9	FOSL1	chr6:31082011-31083367	HCT-116	colon:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
10	NR3C1	chr6:31082362-31082585	A549	lung:	n/a	chr6:31082449-31082458 chr6:31082448-31082457 chr6:31082411-31082418
11	JUND	chr6:31082435-31082518	K562	blood:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082447-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
12	TCF12	chr6:31082110-31082899	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr6:31082158-31082662	MCF-7	breast:	n/a	n/a
14	JUND	chr6:31082259-31082709	A549	lung:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082447-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
15	ZNF143	chr6:31082351-31083154	Hela-S3	cervix:	n/a	n/a
16	RAD21	chr6:31082359-31083165	Hela-S3	cervix:	n/a	chr6:31082419-31082433
17	SMC3	chr6:31082344-31083304	Hela-S3	cervix:	n/a	n/a
18	FOSL2	chr6:31082229-31082710	MCF-7	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
19	MXI1	chr6:31082449-31083233	Hela-S3	cervix:	n/a	n/a
20	FOS	chr6:31082285-31082973	MCF10A-Er-Src	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082458 chr6:31082447-31082459 chr6:31082448-31082458
21	FOSL1	chr6:31082331-31082666	K562	blood:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
22	MYC	chr6:31082421-31082639	MCF10A-Er-Src	breast:	n/a	n/a
23	TCF12	chr6:31081543-31082930	SK-N-SH	brain:	n/a	chr6:31081698-31081708
24	FOS	chr6:31082302-31082682	MCF10A-Er-Src	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082458 chr6:31082447-31082459 chr6:31082448-31082458
25	FOS	chr6:31082297-31082843	MCF10A-Er-Src	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082458 chr6:31082447-31082459 chr6:31082448-31082458
26	MAX	chr6:31082148-31082722	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr6:31082471-31082479	MCF-7	breast:	n/a	n/a
28	FOSL2	chr6:31082314-31082827	MCF-7	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
29	MAX	chr6:31082239-31083001	SK-N-SH	brain:	n/a	n/a
30	STAT3	chr6:31082391-31083054	MCF10A-Er-Src	breast:	n/a	n/a
31	JUND	chr6:31081657-31082959	SK-N-SH	brain:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31081792-31081799 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082447-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
32	JUND	chr6:31082351-31082509	HepG2	liver:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082447-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
33	POLR2A	chr6:31082304-31082513	A549	lung:	n/a	n/a
34	USF2	chr6:31082321-31082636	Hela-S3	cervix:	n/a	n/a
35	FOSL2	chr6:31082237-31082651	HepG2	liver:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
36	POLR2A	chr6:31082269-31082670	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr6:31082307-31082665	HUVEC	blood vessel:	n/a	n/a
38	FOS	chr6:31082084-31082732	HUVEC	blood vessel:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082458 chr6:31082447-31082459 chr6:31082448-31082458
39	POLR2A	chr6:31082388-31083047	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr6:31082350-31083008	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr6:31082441-31083071	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr6:31082218-31082887	SK-N-SH	brain:	n/a	n/a
43	SMARCB1	chr6:31082078-31082664	Hela-S3	cervix:	n/a	chr6:31082449-31082458
44	RAD21	chr6:31082333-31082616	IMR90	lung:	n/a	chr6:31082419-31082433
45	MAZ	chr6:31082377-31083152	Hela-S3	cervix:	n/a	n/a
46	NFIC	chr6:31082177-31082709	ECC-1	luminal epithelium:	n/a	n/a
47	NR3C1	chr6:31082319-31082672	A549	lung:	n/a	chr6:31082449-31082458 chr6:31082448-31082457 chr6:31082411-31082418
48	CHD2	chr6:31082207-31083041	Hela-S3	cervix:	n/a	n/a
49	JUND	chr6:31081759-31082848	SK-N-SH	brain:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31081792-31081799 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082447-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
50	CEBPB	chr6:31082392-31082645	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31080693..31083957-chr6:31087484..31089976,3	K562	blood:
2	chr6:30850897..30852602-chr6:31080609..31083224,2	MCF-7	breast:
3	chr6:31079457..31085209-chr6:31085850..31092700,13	MCF-7	breast:
4	chr6:30882036..30883658-chr6:31081525..31084682,3	MCF-7	breast:
5	chr6:31050562..31052756-chr6:31081245..31083912,2	MCF-7	breast:

Variant related genes	Relation type
PSORS1C1	TF binding region
C6orf15	TF binding region
ENSG00000137411	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000204539	Chromatin interaction
ENSG00000222895	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11756797	0.96[ASN][1000 genomes]
rs17190526	1.00[ASN][1000 genomes]
rs17190589	0.93[ASN][1000 genomes]
rs2233947	0.82[ASN][1000 genomes]
rs3094216	0.97[EUR][1000 genomes]
rs3094220	0.97[EUR][1000 genomes]
rs3095298	0.97[EUR][1000 genomes]
rs3130564	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3130976	0.92[EUR][1000 genomes]
rs3131006	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3132568	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62399065	0.82[ASN][1000 genomes]
rs62399066	0.82[ASN][1000 genomes]
rs9263708	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9263733	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv1033227	chr6:31071547-31101674	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv601490	chr6:31079264-31084435	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	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
14	nsv462747	chr6:31082361-31092124	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv601491	chr6:31082361-31092124	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3095300	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3095300	MICB	cis	cerebellar cortex	BrainEAC
rs3095300	MICB	cis	brain	BrainEAC

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31077600-31082600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:31079600-31082800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr6:31080600-31083800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:31081000-31083200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr6:31081200-31082600	Enhancers	Adipose Nuclei	Adipose
6	chr6:31081200-31082600	Enhancers	Stomach Mucosa	stomach
7	chr6:31081200-31082800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:31081200-31082800	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr6:31081200-31083200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr6:31081200-31083400	Enhancers	Brain Hippocampus Middle	brain
11	chr6:31081200-31083400	Enhancers	Brain Substantia Nigra	brain
12	chr6:31081200-31085400	Enhancers	Right Ventricle	heart
13	chr6:31081400-31082600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:31081400-31082600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:31081400-31083800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:31081600-31082600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr6:31081600-31082600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:31081600-31082800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:31081600-31082800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:31081600-31082800	Enhancers	Brain Angular Gyrus	brain
21	chr6:31081600-31083000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr6:31081600-31083200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr6:31081600-31083400	Enhancers	Brain Cingulate Gyrus	brain
24	chr6:31081600-31083600	Bivalent Enhancer	Placenta	Placenta
25	chr6:31081600-31084000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:31081600-31085400	Enhancers	Lung	lung
27	chr6:31081800-31082800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:31081800-31083200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:31081800-31083200	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr6:31081800-31083200	Enhancers	Fetal Muscle Leg	muscle
31	chr6:31081800-31083200	Bivalent Enhancer	Fetal Stomach	stomach
32	chr6:31081800-31083400	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr6:31081800-31083400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:31081800-31083400	Enhancers	Left Ventricle	heart
35	chr6:31081800-31084000	Flanking Active TSS	Hela-S3	cervix
36	chr6:31081800-31085400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:31082000-31082600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
38	chr6:31082000-31082800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr6:31082000-31083000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr6:31082000-31083200	Bivalent Enhancer	HepG2	liver
41	chr6:31082000-31083400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:31082000-31083600	Enhancers	Ovary	ovary
43	chr6:31082200-31082600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr6:31082200-31082600	Flanking Active TSS	Esophagus	oesophagus
45	chr6:31082200-31082800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:31082200-31082800	Enhancers	Pancreas	Pancrea
47	chr6:31082200-31083000	Enhancers	H9 Cell Line	embryonic stem cell
48	chr6:31082200-31083000	Flanking Active TSS	NHLF	lung
49	chr6:31082200-31083200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:31082200-31083200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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