Variant report

Variant	rs45509595
Chromosome Location	chr6:27840926-27840927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:148)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:148 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27840719-27841475	Gliobla	brain:	n/a	n/a
2	MAX	chr6:27840900-27841941	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr6:27838549-27841707	PANC-1	pancreas:	n/a	n/a
4	SIN3AK20	chr6:27840573-27841694	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr6:27838747-27841649	PBDE	blood:	n/a	n/a
6	CHD1	chr6:27839408-27841329	GM12878	blood:	n/a	n/a
7	JUND	chr6:27840885-27841439	H1-hESC	embryonic stem cell:	n/a	n/a
8	MTA3	chr6:27838567-27841844	GM12878	blood:	n/a	n/a
9	TCF12	chr6:27840805-27841847	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr6:27840535-27841450	GM12878	blood:	n/a	n/a
11	RXRA	chr6:27840921-27841735	SK-N-SH	brain:	n/a	n/a
12	RELA	chr6:27838795-27841703	GM10847	blood:	n/a	n/a
13	TCF3	chr6:27840710-27841440	GM12878	blood:	n/a	n/a
14	TCF12	chr6:27840914-27841722	SK-N-SH	brain:	n/a	n/a
15	NFIC	chr6:27839175-27841922	GM12878	blood:	n/a	n/a
16	ELF1	chr6:27840782-27841460	GM12878	blood:	n/a	n/a
17	MAX	chr6:27840885-27841856	A549	lung:	n/a	n/a
18	RELA	chr6:27839203-27841750	GM18505	blood:	n/a	n/a
19	POLR2A	chr6:27840553-27841408	GM12878	blood:	n/a	n/a
20	POU2F2	chr6:27840863-27841395	GM12878	blood:	n/a	n/a
21	POU2F2	chr6:27840811-27841466	GM12891	blood:	n/a	n/a
22	MAX	chr6:27840791-27841913	SK-N-SH	brain:	n/a	n/a
23	CREB1	chr6:27840532-27841651	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr6:27838660-27841777	GM12891	blood:	n/a	n/a
25	TCF7L2	chr6:27840521-27841640	PANC-1	pancreas:	n/a	n/a
26	REST	chr6:27840843-27841511	SK-N-SH	brain:	n/a	n/a
27	CHD2	chr6:27840592-27841658	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr6:27838847-27841489	GM12892	blood:	n/a	n/a
29	POLR2A	chr6:27840368-27841478	GM12892	blood:	n/a	n/a
30	IRF4	chr6:27840401-27841431	GM12878	blood:	n/a	n/a
31	TAF7	chr6:27840792-27841466	H1-hESC	embryonic stem cell:	n/a	n/a
32	YY1	chr6:27840846-27841749	GM12878	blood:	n/a	chr6:27841631-27841653
33	ATF2	chr6:27840407-27841465	GM12878	blood:	n/a	n/a
34	NFATC1	chr6:27840432-27841588	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:27840504-27841434	U87	brain:	n/a	n/a
36	POLR2A	chr6:27840497-27841548	ProgFib	skin:	n/a	n/a
37	TAF1	chr6:27840806-27841846	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr6:27838335-27841780	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr6:27840884-27841369	A549	lung:	n/a	n/a
40	POLR2A	chr6:27839052-27841717	HUVEC	blood vessel:	n/a	n/a
41	ELF1	chr6:27840780-27841448	GM12878	blood:	n/a	n/a
42	EP300	chr6:27840783-27841586	GM12878	blood:	n/a	n/a
43	POLR2A	chr6:27838719-27841562	GM18951	blood:	n/a	n/a
44	POLR2A	chr6:27838702-27841553	GM19099	blood:	n/a	n/a
45	GATA1	chr6:27838875-27842026	PBDE	blood:	n/a	chr6:27839447-27839463 chr6:27839450-27839460 chr6:27839451-27839460 chr6:27839449-27839461
46	TCF12	chr6:27840692-27841860	A549	lung:	n/a	n/a
47	POLR2A	chr6:27840666-27841496	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr6:27838742-27841834	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr6:27840842-27841419	A549	lung:	n/a	n/a
50	RELA	chr6:27840559-27841757	GM18951	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26053886..26056754-chr6:27838528..27841562,3	MCF-7	breast:
2	chr6:27840835..27841407-chr8:37619758..37620713,2	NB4	blood:
3	chr1:149813872..149815940-chr6:27838697..27841107,2	MCF-7	breast:
4	chr6:26044692..26047309-chr6:27838299..27842021,15	MCF-7	breast:
5	chr6:26031607..26034880-chr6:27837430..27841431,3	K562	blood:
6	chr6:26044526..26047786-chr6:27838310..27841317,7	MCF-7	breast:
7	chr6:26055713..26057538-chr6:27839787..27841318,2	MCF-7	breast:
8	chr6:26123538..26126463-chr6:27839841..27841380,2	MCF-7	breast:
9	chr6:26030829..26032499-chr6:27840625..27843168,2	MCF-7	breast:
10	chr16:56965900..56966477-chr6:27840798..27841399,2	NB4	blood:
11	chr6:27840732..27841298-chr6:27858553..27859054,2	NB4	blood:
12	chr6:26025188..26029060-chr6:27836295..27841543,4	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H3I	TF binding region
ENSG00000180573	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000147471	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000220323	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000051108	Chromatin interaction
ENSG00000183558	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000124529	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs13192965	0.83[EUR][1000 genomes]
rs13193295	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13193480	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13193542	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13194781	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13195728	0.96[EUR][1000 genomes]
rs13199649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13199772	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13199906	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13200214	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13202291	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13202295	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13210634	0.83[EUR][1000 genomes]
rs13212318	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13212651	1.00[EUR][1000 genomes]
rs13215275	0.83[EUR][1000 genomes]
rs13216117	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13217620	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13218875	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs175597	0.90[EUR][1000 genomes]
rs17695758	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17749927	0.83[EUR][1000 genomes]
rs17750747	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17751184	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17763089	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs188015	0.81[EUR][1000 genomes]
rs200481	0.86[EUR][1000 genomes]
rs200482	0.85[EUR][1000 genomes]
rs200483	0.86[EUR][1000 genomes]
rs200485	0.86[EUR][1000 genomes]
rs200489	0.86[EUR][1000 genomes]
rs200490	0.85[EUR][1000 genomes]
rs200493	0.82[EUR][1000 genomes]
rs200497	0.85[EUR][1000 genomes]
rs200501	0.86[EUR][1000 genomes]
rs200948	0.90[EUR][1000 genomes]
rs200949	0.82[EUR][1000 genomes]
rs200950	0.90[EUR][1000 genomes]
rs200952	0.90[EUR][1000 genomes]
rs200953	0.88[EUR][1000 genomes]
rs200954	0.90[EUR][1000 genomes]
rs200977	0.90[EUR][1000 genomes]
rs200981	0.88[EUR][1000 genomes]
rs200983	0.88[EUR][1000 genomes]
rs200989	0.90[EUR][1000 genomes]
rs200990	0.88[EUR][1000 genomes]
rs200992	0.83[EUR][1000 genomes]
rs200995	0.90[EUR][1000 genomes]
rs200996	0.88[EUR][1000 genomes]
rs201002	0.88[EUR][1000 genomes]
rs2747054	0.86[EUR][1000 genomes]
rs28360499	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34064842	0.85[EUR][1000 genomes]
rs34194357	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34295134	0.88[EUR][1000 genomes]
rs34409918	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34432857	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34706883	0.96[EUR][1000 genomes]
rs34718920	0.96[EUR][1000 genomes]
rs34788973	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35037868	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35202262	1.00[AFR][1000 genomes]
rs35339855	1.00[AFR][1000 genomes]
rs35501037	0.89[EUR][1000 genomes]
rs35819751	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs36101351	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36116761	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs370155	0.85[EUR][1000 genomes]
rs390764	0.86[EUR][1000 genomes]
rs401754	0.86[EUR][1000 genomes]
rs425335	1.00[AFR][1000 genomes]
rs483143	0.88[EUR][1000 genomes]
rs493161	0.90[EUR][1000 genomes]
rs557042	0.90[EUR][1000 genomes]
rs56405707	0.83[EUR][1000 genomes]
rs61742093	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66868086	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67040724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67101035	0.96[EUR][1000 genomes]
rs71537572	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71559038	0.82[EUR][1000 genomes]
rs71559050	0.96[EUR][1000 genomes]
rs71559054	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72845070	0.83[EUR][1000 genomes]
rs72847313	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9368531	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs45509595	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs45509595	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs45509595	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27838200-27842000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:27838600-27842400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr6:27838800-27841000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:27838800-27841400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:27838800-27842400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:27839000-27841400	Active TSS	H1 Cell Line	embryonic stem cell
7	chr6:27839000-27841400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr6:27839000-27841400	Active TSS	Fetal Kidney	kidney
9	chr6:27839000-27841600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:27839000-27842200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:27839000-27842200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:27839000-27842400	Active TSS	Thymus	Thymus
13	chr6:27839000-27842800	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:27839200-27841400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:27839200-27841400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:27839200-27841600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:27839200-27841600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:27839200-27841800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:27839200-27842000	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr6:27839200-27842200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr6:27839400-27841200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:27839400-27841200	Active TSS	A549	lung
23	chr6:27839400-27841400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:27839400-27841600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:27839400-27841600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:27839400-27841600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:27839400-27841800	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr6:27839400-27841800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
29	chr6:27839400-27841800	Active TSS	Fetal Brain Female	brain
30	chr6:27839400-27842000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr6:27839600-27841000	Active TSS	Aorta	Aorta
32	chr6:27839600-27841000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
33	chr6:27839600-27841000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:27839600-27841000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
35	chr6:27839600-27841000	Active TSS	Gastric	stomach
36	chr6:27839600-27841400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:27839600-27841400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
38	chr6:27839600-27841400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
39	chr6:27839600-27841800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
40	chr6:27839600-27841800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
41	chr6:27839600-27841800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
42	chr6:27839800-27841000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:27839800-27841000	Active TSS	Liver	Liver
44	chr6:27839800-27841000	Active TSS	Duodenum Mucosa	Duodenum
45	chr6:27839800-27841000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr6:27839800-27841000	Active TSS	Fetal Brain Male	brain
47	chr6:27839800-27841000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
48	chr6:27839800-27841000	Active TSS	Placenta	Placenta
49	chr6:27839800-27841000	Active TSS	Stomach Mucosa	stomach
50	chr6:27839800-27841200	Active TSS	Primary monocytes fromperipheralblood	blood

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