Variant report

Variant	rs35339855
Chromosome Location	chr6:27799520-27799521
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:267)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:267 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27798229-27799532	NB4	blood:	n/a	n/a
2	SIN3AK20	chr6:27798918-27799619	HepG2	liver:	n/a	n/a
3	SP1	chr6:27798987-27799667	K562	blood:	n/a	chr6:27799416-27799428 chr6:27799429-27799440 chr6:27799426-27799440 chr6:27799416-27799427 chr6:27799417-27799426 chr6:27799430-27799439
4	NR2F2	chr6:27798166-27799777	K562	blood:	n/a	n/a
5	CHD2	chr6:27799322-27799771	K562	blood:	n/a	chr6:27799359-27799366
6	MAX	chr6:27799244-27799533	K562	blood:	n/a	n/a
7	TAF1	chr6:27798345-27799635	H1-hESC	embryonic stem cell:	n/a	n/a
8	CHD2	chr6:27798344-27799654	Hela-S3	cervix:	n/a	chr6:27799359-27799366
9	GABPA	chr6:27799041-27799562	Hela-S3	cervix:	n/a	n/a
10	PAX5	chr6:27798100-27799610	GM12878	blood:	n/a	n/a
11	ATF2	chr6:27799216-27799612	GM12878	blood:	n/a	n/a
12	MYBL2	chr6:27798318-27799892	HepG2	liver:	n/a	n/a
13	POU2F2	chr6:27798284-27799551	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:27796831-27799711	H1-hESC	embryonic stem cell:	n/a	n/a
15	HEY1	chr6:27798181-27799703	HepG2	liver:	n/a	n/a
16	BCLAF1	chr6:27799198-27799812	K562	blood:	n/a	n/a
17	ZBTB33	chr6:27798521-27799524	GM12878	blood:	n/a	n/a
18	POU2F2	chr6:27798413-27799548	GM12891	blood:	n/a	n/a
19	TCF12	chr6:27798998-27799625	HepG2	liver:	n/a	chr6:27799455-27799462
20	POLR2A	chr6:27798058-27799530	GM12878	blood:	n/a	n/a
21	CUX1	chr6:27799483-27799862	K562	blood:	n/a	chr6:27799819-27799833 chr6:27799739-27799748 chr6:27799740-27799754
22	POLR2A	chr6:27798000-27799703	HepG2	liver:	n/a	n/a
23	EP300	chr6:27799178-27799714	A549	lung:	n/a	n/a
24	REST	chr6:27799214-27799556	A549	lung:	n/a	n/a
25	CEBPD	chr6:27799224-27799523	HepG2	liver:	n/a	n/a
26	NFIC	chr6:27798295-27799744	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:27797760-27799531	GM12878	blood:	n/a	n/a
28	STAT3	chr6:27799283-27799545	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr6:27798291-27799523	GM12878	blood:	n/a	n/a
30	CHD2	chr6:27799159-27799540	GM12878	blood:	n/a	chr6:27799359-27799366
31	EP300	chr6:27799323-27799531	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:27798215-27799532	Hela-S3	cervix:	n/a	n/a
33	ZBTB33	chr6:27798589-27799657	HepG2	liver:	n/a	n/a
34	TCF3	chr6:27798386-27799520	GM12878	blood:	n/a	n/a
35	STAT3	chr6:27799301-27799636	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr6:27797455-27799646	SK-N-SH	brain:	n/a	n/a
37	GABPA	chr6:27799313-27799578	A549	lung:	n/a	n/a
38	SPI1	chr6:27799096-27799530	GM12891	blood:	n/a	n/a
39	TCF7L2	chr6:27799312-27799534	Hela-S3	cervix:	n/a	n/a
40	MAZ	chr6:27799320-27799529	K562	blood:	n/a	n/a
41	MAZ	chr6:27799271-27799521	Hela-S3	cervix:	n/a	n/a
42	TAF1	chr6:27798935-27799628	A549	lung:	n/a	n/a
43	POLR2A	chr6:27798921-27799572	PANC-1	pancreas:	n/a	n/a
44	SIN3AK20	chr6:27798898-27799544	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:27798153-27799667	HepG2	liver:	n/a	n/a
46	TAF1	chr6:27798918-27799569	GM12892	blood:	n/a	n/a
47	RCOR1	chr6:27798186-27799690	Hela-S3	cervix:	n/a	n/a
48	BCLAF1	chr6:27799210-27799623	GM12878	blood:	n/a	n/a
49	STAT3	chr6:27799311-27799650	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr6:27796592-27807059	K562	blood:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27796630..27800125-chr6:28302655..28305022,3	K562	blood:
2	chr1:150121553..150123075-chr6:27798165..27799927,2	MCF-7	breast:
3	chr6:27798954..27801175-chr6:28191953..28194580,2	K562	blood:
4	chr6:27104100..27108145-chr6:27797427..27800059,3	K562	blood:
5	chr6:26155325..26157964-chr6:27797146..27799688,3	MCF-7	breast:
6	chr6:27797717..27799808-chr9:127629757..127631967,2	K562	blood:
7	chr6:26187875..26189403-chr6:27797113..27800006,2	MCF-7	breast:
8	chr6:26053058..26056960-chr6:27797302..27800295,3	MCF-7	breast:
9	chr6:27798350..27799895-chr6:34855095..34857385,2	K562	blood:
10	chr6:27796980..27799834-chr6:28103780..28105751,2	K562	blood:
11	chr6:27098287..27103463-chr6:27796109..27800380,7	K562	blood:
12	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
13	chr6:26122973..26125036-chr6:27798042..27800567,2	MCF-7	breast:
14	chr6:27798054..27799666-chr7:102036106..102037763,2	MCF-7	breast:
15	chr6:27798199..27799834-chr6:28104251..28105914,2	K562	blood:
16	chr6:27782776..27783687-chr6:27798847..27799701,2	NB4	blood:
17	chr6:26025221..26028451-chr6:27796635..27801025,4	K562	blood:
18	chr6:27217724..27219322-chr6:27799079..27801494,2	MCF-7	breast:
19	chr6:26025403..26028129-chr6:27797100..27800385,4	MCF-7	breast:
20	chr6:27113131..27119021-chr6:27794877..27801018,12	K562	blood:
21	chr6:27798534..27801249-chrX:16803484..16805157,2	MCF-7	breast:
22	chr6:26251146..26253311-chr6:27798112..27799639,2	MCF-7	breast:
23	chr6:27798625..27800434-chr6:28302917..28305015,2	K562	blood:

No data

Variant related genes	Relation type
HIST1H4K	TF binding region
ENSG00000197459	Chromatin interaction
ENSG00000128563	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000064999	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000086712	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000136950	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000064995	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000188987	Chromatin interaction
ENSG00000184825	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13193480	1.00[AFR][1000 genomes]
rs13193542	1.00[AFR][1000 genomes]
rs13194781	1.00[AFR][1000 genomes]
rs13199649	1.00[AFR][1000 genomes]
rs13199772	1.00[AFR][1000 genomes]
rs13199906	1.00[AFR][1000 genomes]
rs13202291	1.00[AFR][1000 genomes]
rs13202295	1.00[AFR][1000 genomes]
rs13212318	1.00[AFR][1000 genomes]
rs13217620	1.00[AFR][1000 genomes]
rs13218875	1.00[AFR][1000 genomes]
rs17695758	1.00[AFR][1000 genomes]
rs17750747	1.00[AFR][1000 genomes]
rs17751184	1.00[AFR][1000 genomes]
rs17763089	1.00[AFR][1000 genomes]
rs34194357	1.00[AFR][1000 genomes]
rs34409918	1.00[AFR][1000 genomes]
rs34432857	1.00[AFR][1000 genomes]
rs35037868	1.00[AFR][1000 genomes]
rs35202262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35819751	1.00[AFR][1000 genomes]
rs36116761	1.00[AFR][1000 genomes]
rs425335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45509595	1.00[AFR][1000 genomes]
rs67040724	1.00[AFR][1000 genomes]
rs72847313	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35339855	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs35339855	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs35339855	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27793400-27803200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:27797200-27799600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:27797200-27799600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:27797200-27799600	Active TSS	Brain Germinal Matrix	brain
5	chr6:27797200-27799800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr6:27797400-27799600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr6:27797400-27799600	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:27797400-27799800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:27797600-27799600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr6:27797600-27799600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:27797600-27799600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr6:27797600-27799600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:27797600-27799600	Active TSS	Thymus	Thymus
14	chr6:27797600-27799800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:27797600-27799800	Active TSS	Rectal Smooth Muscle	rectum
16	chr6:27797600-27799800	Active TSS	HMEC	breast
17	chr6:27797600-27799800	Active TSS	NHLF	lung
18	chr6:27797800-27799600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:27797800-27799800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:27797800-27799800	Active TSS	Brain Anterior Caudate	brain
21	chr6:27797800-27799800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:27797800-27799800	Active TSS	Fetal Intestine Large	intestine
23	chr6:27797800-27799800	Active TSS	Stomach Smooth Muscle	stomach
24	chr6:27797800-27800200	Active TSS	GM12878-XiMat	blood
25	chr6:27798000-27799600	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr6:27798000-27799600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:27798000-27799800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:27798000-27799800	Active TSS	Fetal Thymus	thymus
29	chr6:27798000-27799800	Active TSS	NHDF-Ad	bronchial
30	chr6:27798200-27799600	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr6:27798200-27799600	Active TSS	Brain Substantia Nigra	brain
32	chr6:27798200-27799600	Active TSS	Hela-S3	cervix
33	chr6:27798200-27799600	Active TSS	HSMM	muscle
34	chr6:27798200-27799800	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr6:27798200-27799800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
36	chr6:27798200-27799800	Active TSS	Fetal Muscle Trunk	muscle
37	chr6:27798400-27799600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:27798400-27799600	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr6:27798400-27799600	Active TSS	Aorta	Aorta
40	chr6:27798400-27799600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
41	chr6:27798400-27799600	Active TSS	Stomach Mucosa	stomach
42	chr6:27798400-27799800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr6:27798400-27799800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:27798400-27799800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:27798400-27799800	Active TSS	HSMMtube	muscle
46	chr6:27798600-27799600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:27798600-27799600	Active TSS	Fetal Kidney	kidney
48	chr6:27798600-27799600	Active TSS	Placenta Amnion	Placenta Amnion
49	chr6:27798600-27799600	Active TSS	Dnd41	blood
50	chr6:27798600-27799600	Active TSS	Osteobl	bone

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