Variant report

Variant	rs3175123
Chromosome Location	chr6:27778982-27778983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:139)
CpG islands
(count:0)
Chromatin interactive
region (count:51)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:139 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27777531-27779032	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr6:27777494-27779246	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr6:27774575-27779531	GM12891	blood:	n/a	n/a
4	POLR2A	chr6:27777619-27779456	GM19193	blood:	n/a	n/a
5	POLR2A	chr6:27777602-27779564	GM19099	blood:	n/a	n/a
6	KAT2A	chr6:27777589-27779018	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:27777500-27779550	GM12892	blood:	n/a	n/a
8	POLR2A	chr6:27777630-27779440	GM18526	blood:	n/a	n/a
9	TEAD4	chr6:27777506-27779219	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:27774382-27779662	K562	blood:	n/a	n/a
11	UBTF	chr6:27777312-27779277	K562	blood:	n/a	n/a
12	MAFK	chr6:27777581-27779412	Hela-S3	cervix:	n/a	chr6:27778902-27778917
13	POLR2A	chr6:27777506-27779171	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr6:27777524-27779571	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZBTB33	chr6:27777451-27779238	SK-N-SH	brain:	n/a	n/a
16	PML	chr6:27777518-27779022	MCF-7	breast:	n/a	chr6:27777813-27777821
17	RELA	chr6:27777646-27779015	GM18505	blood:	n/a	n/a
18	RELA	chr6:27777628-27779000	GM18951	blood:	n/a	n/a
19	POLR2A	chr6:27777470-27779491	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:27776232-27779525	K562	blood:	n/a	n/a
21	PML	chr6:27776216-27781822	K562	blood:	n/a	chr6:27777813-27777821
22	POLR2A	chr6:27777655-27779082	HepG2	liver:	n/a	n/a
23	POLR2A	chr6:27774441-27779690	PBDE	blood:	n/a	n/a
24	RELA	chr6:27777643-27779068	GM19193	blood:	n/a	n/a
25	POLR2A	chr6:27777617-27779402	GM12891	blood:	n/a	n/a
26	POLR2A	chr6:27774778-27779424	MCF10A-Er-Src	breast:	n/a	n/a
27	TBL1XR1	chr6:27777664-27778988	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:27777636-27779408	GM15510	blood:	n/a	n/a
29	POLR2A	chr6:27774370-27779564	K562	blood:	n/a	n/a
30	POLR2A	chr6:27777577-27779234	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr6:27776207-27781903	K562	blood:	n/a	n/a
32	POLR2A	chr6:27777536-27779127	HUVEC	blood vessel:	n/a	n/a
33	BCLAF1	chr6:27777595-27779005	GM12878	blood:	n/a	chr6:27777604-27777613
34	TAF7	chr6:27776220-27782251	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr6:27777524-27779406	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr6:27777551-27779633	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr6:27774407-27779624	GM12878	blood:	n/a	n/a
38	SIN3AK20	chr6:27777426-27779010	MCF-7	breast:	n/a	n/a
39	POLR2A	chr6:27777555-27779264	HCT-116	colon:	n/a	n/a
40	MAFK	chr6:27778795-27779062	K562	blood:	n/a	chr6:27778902-27778917
41	RELA	chr6:27777594-27779277	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:27777493-27779025	ProgFib	skin:	n/a	n/a
43	POLR2A	chr6:27774157-27784396	MCF-7	breast:	n/a	n/a
44	SIN3AK20	chr6:27777575-27779078	MCF-7	breast:	n/a	n/a
45	TEAD4	chr6:27776216-27781908	K562	blood:	n/a	n/a
46	MAFK	chr6:27778680-27779065	H1-hESC	embryonic stem cell:	n/a	chr6:27778902-27778917
47	POLR2A	chr6:27777569-27779353	GM12891	blood:	n/a	n/a
48	SP4	chr6:27777176-27779114	H1-hESC	embryonic stem cell:	n/a	chr6:27778702-27778718
49	MTA3	chr6:27777586-27779312	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:27777290-27779481	K562	blood:	n/a	n/a

No data

(count:51 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr12:120637307..120638899-chr6:27776878..27779705,2	K562	blood:
2	chr6:26283778..26286024-chr6:27778308..27780342,2	MCF-7	breast:
3	chr6:27613028..27615946-chr6:27777925..27779442,2	K562	blood:
4	chr6:26122455..26127911-chr6:27777953..27784057,9	MCF-7	breast:
5	chr2:38977199..38979855-chr6:27777911..27779523,2	MCF-7	breast:
6	chr5:137802010..137804655-chr6:27778426..27781380,2	K562	blood:
7	chr6:27173443..27175541-chr6:27778725..27781351,2	K562	blood:
8	chr6:26183066..26187877-chr6:27774821..27779151,5	MCF-7	breast:
9	chr6:27112242..27117659-chr6:27770082..27780470,17	MCF-7	breast:
10	chr20:55842417..55844076-chr6:27778109..27779862,2	MCF-7	breast:
11	chr6:27776967..27779185-chr6:28109334..28112184,3	K562	blood:
12	chr6:27093369..27111594-chr6:27770152..27782376,64	K562	blood:
13	chr6:27776463..27779000-chr6:28890031..28892525,2	MCF-7	breast:
14	chr6:26020721..26023023-chr6:27777113..27779197,2	MCF-7	breast:
15	chr6:26198826..26200652-chr6:27777401..27778996,2	K562	blood:
16	chr1:43432788..43434781-chr6:27778391..27780462,2	MCF-7	breast:
17	chr6:26282374..26290542-chr6:27772727..27779446,9	MCF-7	breast:
18	chr6:26033235..26035308-chr6:27778375..27781238,2	MCF-7	breast:
19	chr6:26021671..26023816-chr6:27777999..27780060,2	MCF-7	breast:
20	chr6:27778583..27780437-chr6:27901055..27904160,3	K562	blood:
21	chr6:26239694..26242322-chr6:27777382..27779315,2	MCF-7	breast:
22	chr6:27778740..27781268-chr6:30683487..30686226,2	K562	blood:
23	chr6:27098259..27104331-chr6:27773668..27779939,16	MCF-7	breast:
24	chr6:26215420..26218815-chr6:27778137..27782519,4	MCF-7	breast:
25	chr6:26270251..26272974-chr6:27776913..27779571,3	MCF-7	breast:
26	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
27	chr17:57105669..57107774-chr6:27778855..27781686,2	MCF-7	breast:
28	chr12:56551653..56553251-chr6:27776259..27779166,2	MCF-7	breast:
29	chr1:155099451..155102336-chr6:27776687..27779634,2	MCF-7	breast:
30	chr6:26196862..26203126-chr6:27774221..27779033,8	MCF-7	breast:
31	chr6:27094403..27106138-chr6:27772392..27783072,46	MCF-7	breast:
32	chr6:26275391..26278113-chr6:27778905..27781292,2	MCF-7	breast:
33	chr3:9438340..9440609-chr6:27776519..27779236,2	K562	blood:
34	chr6:26025862..26028751-chr6:27778385..27781122,2	MCF-7	breast:
35	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:
36	chr6:27775597..27780846-chr6:28300467..28304976,7	K562	blood:
37	chr17:57913518..57917266-chr6:27775743..27780414,5	MCF-7	breast:
38	chr21:40407439..40410203-chr6:27778670..27781408,2	MCF-7	breast:
39	chr6:26215396..26217408-chr6:27778332..27780053,2	MCF-7	breast:
40	chr6:27778513..27779206-chr7:35840567..35841505,2	Hela-S3	cervix:
41	chr6:27518639..27521498-chr6:27778464..27780715,2	K562	blood:
42	chr6:26157592..26159745-chr6:27777609..27780154,2	MCF-7	breast:
43	chr6:27127171..27129409-chr6:27778202..27780210,2	K562	blood:
44	chr6:27775362..27779371-chr6:28186093..28189957,4	K562	blood:
45	chr6:26054474..26058085-chr6:27777303..27780745,6	MCF-7	breast:
46	chr6:27778322..27779984-chr6:28071319..28073386,2	K562	blood:
47	chr6:27777294..27779689-chr7:138144779..138146981,2	MCF-7	breast:
48	chr6:27111749..27120986-chr6:27774460..27781468,38	K562	blood:
49	chr6:26282088..26283672-chr6:27778250..27780102,2	MCF-7	breast:
50	chr6:26197916..26207803-chr6:27772547..27779655,13	K562	blood:

No data

Variant related genes	Relation type
HIST1H2BM	TF binding region
HIST1H2BL	TF binding region
ENSG00000218690	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000243479	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000217275	Chromatin interaction
ENSG00000197697	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000130675	Chromatin interaction
ENSG00000256018	Chromatin interaction
ENSG00000168137	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000122779	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000198327	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000122545	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10946943	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs1157432	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs12055685	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs12110818	0.84[AFR][1000 genomes]
rs1565334	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs16867916	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs16867976	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16867983	0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs16868156	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs1844435	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2130355	0.84[EUR][1000 genomes]
rs2130356	0.84[EUR][1000 genomes]
rs34452669	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800321	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6906653	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs6920044	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs9295751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9348777	0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9348778	0.89[ASN][1000 genomes]
rs9348780	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9357044	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs9357048	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs9357053	0.84[EUR][1000 genomes]
rs9357054	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap]
rs9366707	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366708	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9368524	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs9368538	0.92[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs9380001	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs9380022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9380024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9393832	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs9393856	0.86[ASN][1000 genomes]
rs9393864	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs9393865	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27774200-27779200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:27774200-27779200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr6:27774200-27779400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:27774200-27779800	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr6:27774200-27779800	Active TSS	Thymus	Thymus
6	chr6:27774200-27779800	Active TSS	A549	lung
7	chr6:27774400-27779000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:27774400-27779200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:27774400-27779200	Active TSS	NHDF-Ad	bronchial
10	chr6:27774400-27780000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr6:27774400-27780000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:27774400-27780000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:27774400-27780000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:27774400-27780200	Active TSS	H1 Cell Line	embryonic stem cell
15	chr6:27774400-27784000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:27774600-27779600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:27775200-27779000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:27775200-27779600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:27775400-27779000	Active TSS	NHEK	skin
20	chr6:27775400-27779800	Active TSS	Fetal Thymus	thymus
21	chr6:27776200-27780000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:27776400-27779600	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr6:27776800-27779000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:27776800-27779200	Active TSS	NHLF	lung
25	chr6:27777400-27779200	Flanking Active TSS	Liver	Liver
26	chr6:27777400-27779600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:27777600-27779000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:27777600-27779000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr6:27777600-27779000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr6:27777600-27779000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
31	chr6:27777600-27779200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:27777600-27779200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:27777800-27779000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:27777800-27779000	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr6:27777800-27779400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:27777800-27779400	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr6:27777800-27779400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:27777800-27780600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr6:27778000-27779000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr6:27778000-27779000	Flanking Active TSS	HMEC	breast
41	chr6:27778000-27779200	Active TSS	Rectal Smooth Muscle	rectum
42	chr6:27778000-27779400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:27778000-27779400	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr6:27778000-27779600	Transcr. at gene 5' and 3'	K562	blood
45	chr6:27778000-27780000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:27778000-27782200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:27778200-27779000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr6:27778200-27779000	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr6:27778200-27779000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr6:27778200-27779000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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