Variant report

Variant	rs6925178
Chromosome Location	chr6:28973215-28973216
allele	A/C
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	STAT5A	chr6:28972926-28973690	K562	blood:	n/a	chr6:28973181-28973189
2	GABPA	chr6:28972841-28973714	HL-60	blood:	n/a	n/a
3	POLR2A	chr6:28973057-28973603	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr6:28973208-28973681	PANC-1	pancreas:	n/a	n/a
5	RCOR1	chr6:28973002-28973631	K562	blood:	n/a	n/a
6	GABPA	chr6:28973072-28973666	HL-60	blood:	n/a	n/a
7	E2F4	chr6:28973000-28973618	MCF10A-Er-Src	breast:	n/a	chr6:28973149-28973156 chr6:28973148-28973157 chr6:28973149-28973156 chr6:28973149-28973156 chr6:28973145-28973157
8	MAX	chr6:28972965-28973589	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr6:28972999-28973247	A549	lung:	n/a	chr6:28973149-28973156 chr6:28973148-28973157 chr6:28973149-28973156 chr6:28973149-28973156 chr6:28973146-28973157 chr6:28973145-28973157
10	MAX	chr6:28973056-28973652	MCF-7	breast:	n/a	n/a
11	E2F6	chr6:28972961-28973570	K562	blood:	n/a	chr6:28973149-28973156 chr6:28973148-28973157 chr6:28973149-28973156 chr6:28973149-28973156 chr6:28973146-28973157 chr6:28973145-28973157
12	TAF1	chr6:28973019-28973643	K562	blood:	n/a	n/a
13	HCFC1	chr6:28973089-28973937	Hela-S3	cervix:	n/a	n/a
14	JUND	chr6:28973031-28973619	K562	blood:	n/a	n/a
15	SP2	chr6:28973024-28973651	H1-hESC	embryonic stem cell:	n/a	n/a
16	UBTF	chr6:28973207-28973608	K562	blood:	n/a	n/a
17	ELF1	chr6:28973020-28973715	MCF-7	breast:	n/a	n/a
18	NR2F2	chr6:28972621-28973792	K562	blood:	n/a	n/a
19	HA-E2F1	chr6:28972942-28973646	MCF-7	breast:	n/a	chr6:28973149-28973156 chr6:28973148-28973157 chr6:28973149-28973156 chr6:28973149-28973156 chr6:28973145-28973157
20	MAX	chr6:28973125-28973612	Hela-S3	cervix:	n/a	n/a
21	MAZ	chr6:28972970-28973660	K562	blood:	n/a	n/a
22	POLR2A	chr6:28971836-28973648	K562	blood:	n/a	n/a
23	MYC	chr6:28972978-28973644	K562	blood:	n/a	n/a
24	POLR2A	chr6:28973064-28973530	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr6:28973180-28973674	PFSK-1	brain:	n/a	n/a
26	HEY1	chr6:28972905-28973623	K562	blood:	n/a	n/a
27	GTF2B	chr6:28973172-28973555	K562	blood:	n/a	n/a
28	POLR2A	chr6:28973158-28973630	Gliobla	brain:	n/a	n/a
29	POLR2A	chr6:28973048-28973594	MCF-7	breast:	n/a	n/a
30	MAX	chr6:28972828-28973679	A549	lung:	n/a	n/a
31	TBL1XR1	chr6:28972989-28973737	K562	blood:	n/a	n/a
32	CBX3	chr6:28972868-28973658	K562	blood:	n/a	chr6:28973644-28973655
33	POLR2A	chr6:28973068-28973716	K562	blood:	n/a	n/a
34	GABPA	chr6:28972758-28973916	MCF-7	breast:	n/a	n/a
35	PML	chr6:28972843-28973743	K562	blood:	n/a	chr6:28973586-28973594
36	STAT3	chr6:28973060-28973586	MCF10A-Er-Src	breast:	n/a	chr6:28973432-28973443 chr6:28973181-28973189
37	MAX	chr6:28973057-28973589	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr6:28973192-28973559	A549	lung:	n/a	n/a
39	POLR2A	chr6:28973069-28973687	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr6:28973054-28973648	U87	brain:	n/a	n/a
41	MAX	chr6:28973006-28973653	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF1	chr6:28973190-28973510	PFSK-1	brain:	n/a	n/a
43	IRF1	chr6:28972992-28973681	K562	blood:	n/a	chr6:28973396-28973405
44	ELF1	chr6:28973097-28973519	K562	blood:	n/a	n/a
45	MAX	chr6:28972814-28973715	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr6:28973013-28973753	K562	blood:	n/a	n/a
47	POLR2A	chr6:28973050-28973704	PBDE	blood:	n/a	n/a
48	POLR2A	chr6:28972810-28973709	K562	blood:	n/a	n/a
49	POLR2A	chr6:28973165-28973716	HUVEC	blood vessel:	n/a	n/a
50	STAT5A	chr6:28973100-28973704	K562	blood:	n/a	chr6:28973181-28973189

No.	Distal block	Cell Line	Cell type
1	chr6:28952766..28954746-chr6:28971481..28973784,3	MCF-7	breast:
2	chr6:28827198..28830005-chr6:28973058..28974944,2	K562	blood:
3	chr6:28830568..28832864-chr6:28971652..28974126,2	K562	blood:
4	chr6:28890160..28893119-chr6:28970726..28976038,6	K562	blood:
5	chr6:28830168..28831847-chr6:28972589..28974401,2	K562	blood:
6	chr6:28948241..28954799-chr6:28970209..28976187,12	MCF-7	breast:
7	chr6:28864176..28867304-chr6:28972657..28975728,3	K562	blood:
8	chr6:28762168..28764957-chr6:28971752..28974125,2	K562	blood:
9	chr6:28890449..28893259-chr6:28971754..28975345,6	K562	blood:

Variant related genes	Relation type
ZNF311	TF binding region
ENSG00000213916	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000265764	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000244349	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs4565335	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6909302	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6918712	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6919044	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6919687	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6923005	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6924824	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6930903	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6933976	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7741520	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7743837	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7744689	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7744795	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7749435	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7764481	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9257445	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9348822	0.86[AFR][1000 genomes]
rs9380105	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461498	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461499	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468473	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9501291	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[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	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv601215	chr6:28946920-29348297	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv1023028	chr6:28956136-29343575	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv538170	chr6:28956136-29343575	ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
15	nsv1018937	chr6:28956136-29366175	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
16	nsv1032468	chr6:28968930-29155749	Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6925178	ZNF323	cis	cerebellum	SCAN
rs6925178	HIST1H2AA	cis	cerebellum	SCAN
rs6925178	HIST1H1A	cis	parietal	SCAN
rs6925178	HIST1H4C	cis	parietal	SCAN
rs6925178	HIST1H4I	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28972000-28973800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:28972400-28973600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:28972400-28973600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:28972400-28973800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:28972600-28973400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:28972600-28973600	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:28972600-28973600	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:28972600-28973600	Active TSS	HSMM	muscle
9	chr6:28972600-28973800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr6:28972600-28973800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr6:28972800-28973400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr6:28972800-28973400	Active TSS	Aorta	Aorta
13	chr6:28972800-28973400	Active TSS	Liver	Liver
14	chr6:28972800-28973600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:28972800-28973600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:28972800-28973600	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr6:28972800-28973600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr6:28972800-28973600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:28972800-28973600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:28972800-28973600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:28972800-28973600	Active TSS	Colonic Mucosa	Colon
22	chr6:28972800-28973600	Active TSS	Fetal Muscle Trunk	muscle
23	chr6:28972800-28973600	Active TSS	Ovary	ovary
24	chr6:28972800-28973600	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr6:28972800-28973600	Active TSS	Right Atrium	heart
26	chr6:28972800-28973600	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr6:28972800-28973600	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr6:28972800-28973600	Active TSS	Hela-S3	cervix
29	chr6:28972800-28973600	Active TSS	HSMMtube	muscle
30	chr6:28972800-28973600	Active TSS	NHDF-Ad	bronchial
31	chr6:28972800-28973600	Active TSS	NHLF	lung
32	chr6:28972800-28973600	Active TSS	Osteobl	bone
33	chr6:28972800-28973800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr6:28972800-28973800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr6:28972800-28973800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:28972800-28973800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
37	chr6:28972800-28973800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:28972800-28973800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:28972800-28973800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:28972800-28973800	Active TSS	Brain Hippocampus Middle	brain
41	chr6:28972800-28973800	Active TSS	Duodenum Mucosa	Duodenum
42	chr6:28972800-28973800	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr6:28972800-28973800	Active TSS	Fetal Intestine Large	intestine
44	chr6:28972800-28973800	Active TSS	Fetal Kidney	kidney
45	chr6:28972800-28973800	Active TSS	Fetal Lung	lung
46	chr6:28972800-28974000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:28973000-28973400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:28973000-28973400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:28973000-28973400	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr6:28973000-28973400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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