Variant report

Variant	rs34718920
Chromosome Location	chr6:27783941-27783942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27781476-27784189	ProgFib	skin:	n/a	n/a
2	PML	chr6:27782350-27784057	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:27781096-27784165	GM18505	blood:	n/a	n/a
4	EP300	chr6:27783666-27783947	GM12878	blood:	n/a	n/a
5	MTA3	chr6:27782365-27783982	GM12878	blood:	n/a	n/a
6	IKZF1	chr6:27783326-27783949	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:27780777-27784258	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:27781293-27783971	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr6:27781474-27784000	Raji	blood:	n/a	n/a
10	MAX	chr6:27782639-27784028	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:27781423-27784034	GM15510	blood:	n/a	n/a
12	POLR2A	chr6:27774157-27784396	MCF-7	breast:	n/a	n/a
13	POLR2A	chr6:27781253-27783998	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:27780977-27784153	GM12891	blood:	n/a	n/a
15	POLR2A	chr6:27781267-27783987	GM12892	blood:	n/a	n/a
16	POLR2A	chr6:27781252-27783997	GM12878	blood:	n/a	n/a
17	STAT1	chr6:27783829-27784026	GM12878	blood:	n/a	n/a
18	BHLHE40	chr6:27783667-27784196	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:27782360-27783998	HUVEC	blood vessel:	n/a	n/a
20	MAX	chr6:27782526-27784036	NB4	blood:	n/a	n/a
21	POLR2A	chr6:27781038-27783955	GM12892	blood:	n/a	n/a
22	POLR2A	chr6:27781310-27784190	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr6:27781643-27784128	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:27782729-27784116	MCF-7	breast:	n/a	n/a
25	MTA3	chr6:27782653-27783961	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:27780326-27784278	PANC-1	pancreas:	n/a	n/a
27	NFATC1	chr6:27782387-27783971	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:27781247-27784072	GM12892	blood:	n/a	n/a
29	POLR2A	chr6:27781626-27784116	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:27781446-27784075	GM19193	blood:	n/a	n/a
31	POLR2A	chr6:27780152-27784269	PANC-1	pancreas:	n/a	n/a
32	CHD1	chr6:27782733-27784355	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:27781033-27784193	GM18526	blood:	n/a	n/a
34	POLR2A	chr6:27781267-27784085	HUVEC	blood vessel:	n/a	n/a
35	NFIC	chr6:27780650-27783972	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:27773907-27784120	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr6:27779891-27784007	PBDE	blood:	n/a	n/a
38	POLR2A	chr6:27780985-27784252	GM19099	blood:	n/a	n/a
39	POLR2A	chr6:27781631-27784132	MCF-7	breast:	n/a	n/a
40	POLR2A	chr6:27781424-27784016	GM10847	blood:	n/a	n/a
41	POLR2A	chr6:27781091-27784109	GM18951	blood:	n/a	n/a
42	STAT5A	chr6:27782377-27783968	GM12878	blood:	n/a	n/a
43	POLR2A	chr6:27781270-27784004	GM12892	blood:	n/a	n/a
44	ATF2	chr6:27782372-27783977	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:27780528-27784231	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26122455..26127911-chr6:27777953..27784057,9	MCF-7	breast:
2	chr6:27100161..27102247-chr6:27781053..27784459,3	MCF-7	breast:
3	chr5:65439509..65441854-chr6:27782836..27785587,2	MCF-7	breast:
4	chr6:26216490..26219190-chr6:27783241..27786059,2	MCF-7	breast:
5	chr6:26155301..26160613-chr6:27781458..27785146,6	MCF-7	breast:
6	chr20:45986636..45989209-chr6:27782881..27785567,2	MCF-7	breast:
7	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
8	chr6:26233018..26235518-chr6:27781228..27784528,3	MCF-7	breast:
9	chr6:27113704..27115641-chr6:27781150..27784385,3	MCF-7	breast:
10	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:
11	chr6:26198554..26201743-chr6:27781165..27784293,4	MCF-7	breast:
12	chr6:26020260..26024010-chr6:27780504..27784636,5	MCF-7	breast:
13	chr6:27154833..27157823-chr6:27782934..27785900,2	K562	blood:
14	chr6:27105231..27107098-chr6:27782990..27785264,2	K562	blood:

No data

Variant related genes	Relation type
HIST1H2AJ	TF binding region
ENSG00000265565	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000124575	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000253744	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000218281	Chromatin interaction
ENSG00000153914	Chromatin interaction
ENSG00000168298	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs13192965	0.87[EUR][1000 genomes]
rs13193295	0.85[EUR][1000 genomes]
rs13193480	0.92[EUR][1000 genomes]
rs13193542	0.92[EUR][1000 genomes]
rs13194781	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13195728	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13199649	0.94[EUR][1000 genomes]
rs13199772	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13199906	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13202291	0.91[EUR][1000 genomes]
rs13202295	0.92[EUR][1000 genomes]
rs13210634	0.87[EUR][1000 genomes]
rs13212318	0.89[EUR][1000 genomes]
rs13212651	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13215275	0.87[EUR][1000 genomes]
rs13216117	0.93[EUR][1000 genomes]
rs13217620	0.87[EUR][1000 genomes]
rs13218875	0.88[EUR][1000 genomes]
rs175597	0.86[EUR][1000 genomes]
rs17695758	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17749927	0.87[EUR][1000 genomes]
rs17750747	0.92[EUR][1000 genomes]
rs17751184	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17763089	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs200481	0.90[EUR][1000 genomes]
rs200482	0.88[EUR][1000 genomes]
rs200483	0.90[EUR][1000 genomes]
rs200485	0.90[EUR][1000 genomes]
rs200489	0.90[EUR][1000 genomes]
rs200490	0.88[EUR][1000 genomes]
rs200493	0.85[EUR][1000 genomes]
rs200497	0.88[EUR][1000 genomes]
rs200501	0.90[EUR][1000 genomes]
rs200948	0.86[EUR][1000 genomes]
rs200950	0.86[EUR][1000 genomes]
rs200952	0.86[EUR][1000 genomes]
rs200953	0.85[EUR][1000 genomes]
rs200954	0.86[EUR][1000 genomes]
rs200977	0.86[EUR][1000 genomes]
rs200981	0.85[EUR][1000 genomes]
rs200983	0.85[EUR][1000 genomes]
rs200989	0.86[EUR][1000 genomes]
rs200990	0.85[EUR][1000 genomes]
rs200995	0.86[EUR][1000 genomes]
rs200996	0.85[EUR][1000 genomes]
rs201002	0.85[EUR][1000 genomes]
rs2747054	0.90[EUR][1000 genomes]
rs28360499	0.91[EUR][1000 genomes]
rs34064842	0.89[EUR][1000 genomes]
rs34194357	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34295134	0.85[EUR][1000 genomes]
rs34409918	0.89[EUR][1000 genomes]
rs34432857	0.89[EUR][1000 genomes]
rs34706883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34788973	0.93[EUR][1000 genomes]
rs35037868	0.92[EUR][1000 genomes]
rs35501037	0.92[EUR][1000 genomes]
rs35715914	0.87[EUR][1000 genomes]
rs35819751	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36101351	0.93[EUR][1000 genomes]
rs36116761	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs370155	0.88[EUR][1000 genomes]
rs390764	0.90[EUR][1000 genomes]
rs401754	0.90[EUR][1000 genomes]
rs45509595	0.96[EUR][1000 genomes]
rs483143	0.85[EUR][1000 genomes]
rs493161	0.86[EUR][1000 genomes]
rs557042	0.86[EUR][1000 genomes]
rs56405707	0.87[EUR][1000 genomes]
rs61742093	0.93[EUR][1000 genomes]
rs66868086	0.96[EUR][1000 genomes]
rs67040724	0.93[EUR][1000 genomes]
rs67101035	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67652222	0.85[EUR][1000 genomes]
rs71537572	0.85[EUR][1000 genomes]
rs71559038	0.85[EUR][1000 genomes]
rs71559050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71559051	0.81[AMR][1000 genomes]
rs71559054	0.93[EUR][1000 genomes]
rs72845046	0.85[EUR][1000 genomes]
rs72845070	0.87[EUR][1000 genomes]
rs72847313	0.92[EUR][1000 genomes]
rs9368531	0.90[EUR][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	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
8	nsv970094	chr6:27782238-27786201	Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	41 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34718920	AL022393.7	cis	Muscle Skeletal	GTEx
rs34718920	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs34718920	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs34718920	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27774400-27784000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:27780200-27784000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:27780800-27784200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:27781000-27784400	Active TSS	Brain Germinal Matrix	brain
5	chr6:27781200-27784000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr6:27781200-27784400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:27781200-27784400	Active TSS	A549	lung
8	chr6:27781600-27784000	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:27781600-27784000	Active TSS	Thymus	Thymus
10	chr6:27781800-27784000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:27781800-27784000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:27782800-27784000	Flanking Active TSS	Fetal Thymus	thymus
13	chr6:27783000-27784000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr6:27783000-27784200	Flanking Active TSS	GM12878-XiMat	blood
15	chr6:27783200-27784000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:27783200-27784000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:27783200-27787600	Weak transcription	Hela-S3	cervix
18	chr6:27783400-27784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:27783400-27784000	Enhancers	Primary B cells from peripheral blood	blood
20	chr6:27783400-27784000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
21	chr6:27783400-27784400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:27783400-27784800	Weak transcription	HepG2	liver
23	chr6:27783400-27791200	Weak transcription	Liver	Liver
24	chr6:27783400-27791800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:27783600-27784000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr6:27783600-27784000	Enhancers	Fetal Stomach	stomach
27	chr6:27783600-27784000	Enhancers	NHDF-Ad	bronchial
28	chr6:27783600-27784800	Weak transcription	Fetal Intestine Small	intestine
29	chr6:27783600-27785200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr6:27783600-27787000	Weak transcription	Right Atrium	heart
31	chr6:27783600-27787600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:27783600-27789400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:27783600-27791000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:27783800-27784000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:27783800-27784000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:27783800-27784000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:27783800-27784000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:27783800-27784200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:27783800-27784200	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr6:27783800-27784400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:27783800-27784800	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr6:27783800-27787400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:27783800-27787800	Weak transcription	Duodenum Mucosa	Duodenum

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