Variant report

Variant	rs9442945
Chromosome Location	chr6:74405752-74405753
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	chr6:74405518-74405765	GM12878	blood:	n/a	n/a
2	MAZ	chr6:74405418-74406459	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:74405498-74405791	A549	lung:	n/a	n/a
4	YY1	chr6:74405568-74406206	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:74405723-74406240	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr6:74405291-74406294	ProgFib	skin:	n/a	n/a
7	FOSL2	chr6:74404666-74405840	A549	lung:	n/a	chr6:74404981-74404989 chr6:74404982-74404989 chr6:74404967-74404979 chr6:74404981-74404989 chr6:74405462-74405470 chr6:74405460-74405472 chr6:74405463-74405474 chr6:74404980-74404990 chr6:74405461-74405472
8	BCL3	chr6:74405337-74405774	GM12878	blood:	n/a	n/a
9	FOS	chr6:74404572-74405877	MCF10A-Er-Src	breast:	n/a	chr6:74404981-74404989 chr6:74404982-74404989 chr6:74404967-74404979 chr6:74404981-74404989 chr6:74405462-74405470 chr6:74405460-74405472 chr6:74405460-74405471 chr6:74405463-74405474 chr6:74404980-74404990
10	POLR2A	chr6:74404665-74406197	U87	brain:	n/a	n/a
11	RAD21	chr6:74405343-74406105	IMR90	lung:	n/a	n/a
12	YY1	chr6:74405488-74405977	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr6:74404841-74406292	IMR90	lung:	n/a	n/a
14	SMARCC1	chr6:74404409-74407235	Hela-S3	cervix:	n/a	chr6:74404981-74404990
15	ZKSCAN1	chr6:74405369-74406266	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:74405354-74406209	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr6:74405404-74406297	Gliobla	brain:	n/a	n/a
18	TCF12	chr6:74405215-74405970	A549	lung:	n/a	chr6:74405544-74405553
19	PBX3	chr6:74404697-74406241	SK-N-SH	brain:	n/a	n/a
20	CEBPB	chr6:74405120-74405844	A549	lung:	n/a	n/a
21	POLR2A	chr6:74405272-74406279	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr6:74405065-74407421	PBDE	blood:	n/a	n/a
23	YY1	chr6:74405353-74406005	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr6:74405358-74406258	Hela-S3	cervix:	n/a	n/a
25	MAX	chr6:74405495-74406185	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr6:74405605-74405835	H1-hESC	embryonic stem cell:	n/a	n/a
27	EP300	chr6:74405153-74406264	ECC-1	luminal epithelium:	n/a	n/a
28	BACH1	chr6:74405363-74406225	H1-hESC	embryonic stem cell:	n/a	chr6:74405459-74405473
29	EP300	chr6:74405109-74405824	A549	lung:	n/a	n/a
30	ZNF143	chr6:74405444-74406094	Hela-S3	cervix:	n/a	n/a
31	CEBPB	chr6:74405212-74406023	A549	lung:	n/a	n/a
32	POLR2A	chr6:74405279-74406369	HUVEC	blood vessel:	n/a	n/a
33	FOXA2	chr6:74405322-74405881	A549	lung:	n/a	n/a
34	RFX5	chr6:74404792-74406101	Hela-S3	cervix:	n/a	n/a
35	E2F1	chr6:74405375-74406248	Hela-S3	cervix:	n/a	n/a
36	FOXA1	chr6:74405292-74405772	HepG2	liver:	n/a	n/a
37	BCL3	chr6:74405115-74405885	A549	lung:	n/a	n/a
38	NR3C1	chr6:74405312-74405779	A549	lung:	n/a	n/a
39	MAX	chr6:74405292-74406339	SK-N-SH	brain:	n/a	n/a
40	TCF12	chr6:74404272-74406206	SK-N-SH	brain:	n/a	chr6:74405544-74405553
41	POLR2A	chr6:74404505-74407290	Hela-S3	cervix:	n/a	n/a
42	NFIC	chr6:74404502-74406380	SK-N-SH	brain:	n/a	n/a
43	KAP1	chr6:74405363-74406371	HEK293	kidney:	n/a	n/a
44	SMC3	chr6:74404974-74406522	Hela-S3	cervix:	n/a	n/a
45	EP300	chr6:74405073-74405940	A549	lung:	n/a	n/a
46	YY1	chr6:74405605-74405832	K562	blood:	n/a	n/a
47	CEBPB	chr6:74405500-74405862	A549	lung:	n/a	n/a
48	YY1	chr6:74405542-74405915	SK-N-SH_RA	brain:	n/a	n/a
49	FOSL2	chr6:74405277-74405775	MCF-7	breast:	n/a	chr6:74405462-74405470 chr6:74405460-74405472 chr6:74405463-74405474 chr6:74405461-74405472
50	POLR2A	chr6:74405276-74406342	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:74405547..74407236-chr6:76311267..76312799,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC17A5-1	chr6:74405555-74405854	ENSG00000231652
2	lnc-SLC17A5-1	chr6:74405555-74405854	ENSG00000231652.2

Variant related genes	Relation type
CD109	TF binding region
ENSG00000112701	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs73754658	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9442948	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs9442950	1.00[MEX][hapmap]
rs9446983	0.95[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9446984	0.85[LWK][hapmap]
rs9446985	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
6	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv1029927	chr6:74300496-74424355	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv1027691	chr6:74302980-74417450	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74404400-74405800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
2	chr6:74404400-74405800	Flanking Active TSS	NH-A	brain
3	chr6:74404400-74406000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:74404600-74407800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:74404800-74406200	Active TSS	Brain Anterior Caudate	brain
6	chr6:74404800-74406600	Active TSS	Aorta	Aorta
7	chr6:74404800-74406800	Active TSS	Stomach Smooth Muscle	stomach
8	chr6:74405000-74406000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
9	chr6:74405000-74406000	Active TSS	Monocytes-CD14+_RO01746	blood
10	chr6:74405000-74406200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
11	chr6:74405000-74406400	Active TSS	Brain Cingulate Gyrus	brain
12	chr6:74405000-74406400	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr6:74405000-74406400	Active TSS	Colon Smooth Muscle	Colon
14	chr6:74405000-74406600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:74405000-74406600	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr6:74405000-74406600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
17	chr6:74405000-74407000	Active TSS	A549	lung
18	chr6:74405000-74407200	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr6:74405000-74407600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:74405000-74408000	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr6:74405200-74405800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:74405200-74405800	Flanking Active TSS	Brain Germinal Matrix	brain
23	chr6:74405200-74405800	Flanking Active TSS	Fetal Muscle Leg	muscle
24	chr6:74405200-74405800	Flanking Active TSS	Fetal Thymus	thymus
25	chr6:74405200-74406200	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr6:74405200-74406200	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr6:74405200-74406200	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr6:74405200-74406200	Bivalent Enhancer	Fetal Brain Male	brain
29	chr6:74405200-74406200	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr6:74405200-74406400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
31	chr6:74405200-74406400	Active TSS	Primary T cells from cord blood	blood
32	chr6:74405200-74406400	Active TSS	Fetal Brain Female	brain
33	chr6:74405200-74406400	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr6:74405200-74406400	Active TSS	Ovary	ovary
35	chr6:74405200-74406400	Active TSS	Psoas Muscle	Psoas
36	chr6:74405200-74406600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr6:74405200-74406600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:74405200-74406600	Active TSS	Rectal Smooth Muscle	rectum
39	chr6:74405200-74406800	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr6:74405200-74406800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:74405200-74406800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:74405200-74406800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:74405200-74406800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:74405200-74406800	Active TSS	Thymus	Thymus
45	chr6:74405200-74406800	Active TSS	HMEC	breast
46	chr6:74405200-74406800	Active TSS	HSMM	muscle
47	chr6:74405200-74407000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:74405200-74407000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:74405200-74407000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:74405200-74407000	Active TSS	Fetal Muscle Trunk	muscle

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