Variant report

Variant	rs6547627
Chromosome Location	chr2:85843035-85843036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:258)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:258 , 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	CREB1	chr2:85842993-85843725	A549	lung:	n/a	n/a
2	SIN3AK20	chr2:85843035-85843532	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAZ	chr2:85843014-85843726	K562	blood:	n/a	n/a
4	POLR2A	chr2:85842992-85843746	U87	brain:	n/a	n/a
5	PBX3	chr2:85842999-85843596	A549	lung:	n/a	chr2:85843249-85843258
6	REST	chr2:85842971-85843708	HL-60	blood:	n/a	n/a
7	YY1	chr2:85843000-85843639	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:85842936-85843713	GM12891	blood:	n/a	n/a
9	GABPA	chr2:85842973-85843540	MCF-7	breast:	n/a	chr2:85843284-85843298
10	POLR2A	chr2:85842962-85843608	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr2:85842938-85843589	HEK293	kidney:	n/a	n/a
12	ETS1	chr2:85843033-85843569	GM12878	blood:	n/a	chr2:85843141-85843156 chr2:85843143-85843156
13	NR2F2	chr2:85842991-85843603	MCF-7	breast:	n/a	n/a
14	FOXM1	chr2:85842936-85843461	GM12878	blood:	n/a	n/a
15	SP4	chr2:85842948-85843654	H1-hESC	embryonic stem cell:	n/a	n/a
16	HDAC2	chr2:85842974-85843532	HepG2	liver:	n/a	chr2:85843265-85843274
17	ATF2	chr2:85842984-85843376	GM12878	blood:	n/a	n/a
18	YY1	chr2:85842947-85843722	HepG2	liver:	n/a	chr2:85843683-85843694
19	SP1	chr2:85842920-85843772	A549	lung:	n/a	chr2:85843683-85843693 chr2:85843688-85843698 chr2:85843239-85843260 chr2:85843684-85843698 chr2:85843682-85843694 chr2:85843682-85843694 chr2:85843679-85843693 chr2:85843683-85843692
20	GATA3	chr2:85842933-85843766	A549	lung:	n/a	n/a
21	POLR2A	chr2:85842986-85843873	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:85842928-85843658	K562	blood:	n/a	n/a
23	SPI1	chr2:85843022-85843308	HL-60	blood:	n/a	chr2:85843144-85843151
24	POLR2A	chr2:85842806-85843710	PFSK-1	brain:	n/a	n/a
25	ELF1	chr2:85843015-85843696	MCF-7	breast:	n/a	n/a
26	POLR2A	chr2:85843013-85843809	HL-60	blood:	n/a	n/a
27	POLR2A	chr2:85842956-85843720	ECC-1	luminal epithelium:	n/a	n/a
28	ZNF143	chr2:85843028-85843501	GM12878	blood:	n/a	n/a
29	CBX3	chr2:85842950-85843780	K562	blood:	n/a	n/a
30	MAX	chr2:85842974-85843855	A549	lung:	n/a	n/a
31	POLR2A	chr2:85843005-85843623	K562	blood:	n/a	n/a
32	GATA3	chr2:85843029-85843737	MCF-7	breast:	n/a	n/a
33	HEY1	chr2:85843018-85843661	HepG2	liver:	n/a	n/a
34	YY1	chr2:85843029-85843563	SK-N-SH_RA	brain:	n/a	n/a
35	SPI1	chr2:85843028-85843280	K562	blood:	n/a	chr2:85843144-85843151
36	NR3C1	chr2:85843011-85843384	A549	lung:	n/a	n/a
37	STAT5A	chr2:85842993-85843536	GM12878	blood:	n/a	n/a
38	ZBTB33	chr2:85842991-85843587	HepG2	liver:	n/a	chr2:85843341-85843356
39	TBL1XR1	chr2:85843031-85843515	K562	blood:	n/a	n/a
40	POLR2A	chr2:85842964-85843707	K562	blood:	n/a	n/a
41	ATF3	chr2:85842953-85843501	A549	lung:	n/a	n/a
42	PML	chr2:85842942-85843719	GM12878	blood:	n/a	n/a
43	PML	chr2:85842941-85843723	K562	blood:	n/a	n/a
44	TAF1	chr2:85842976-85843768	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr2:85842998-85843665	GM12878	blood:	n/a	n/a
46	SIN3AK20	chr2:85843026-85843716	SK-N-SH	brain:	n/a	n/a
47	MAX	chr2:85842958-85843886	HepG2	liver:	n/a	n/a
48	ZBTB33	chr2:85842960-85843549	HepG2	liver:	n/a	chr2:85843341-85843356
49	YY1	chr2:85843005-85843511	K562	blood:	n/a	n/a
50	MAX	chr2:85843017-85843796	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85788038..85789914-chr2:85841678..85843321,2	MCF-7	breast:
2	chr2:85581050..85582551-chr2:85842255..85845112,2	K562	blood:
3	chr2:85764278..85767937-chr2:85842194..85845131,5	K562	blood:
4	chr2:85554801..85556928-chr2:85841826..85844560,3	K562	blood:
5	chr2:85635586..85637613-chr2:85842504..85845075,3	K562	blood:
6	chr2:85635586..85637613-chr2:85842504..85845075,2	K562	blood:
7	chr1:28831848..28832533-chr2:85842857..85843786,2	HCT-116	colon:
8	chr2:85842186..85844558-chr2:85848833..85852052,4	MCF-7	breast:
9	chr2:85643378..85649324-chr2:85837656..85846268,13	K562	blood:
10	chr2:85765143..85767907-chr2:85841259..85844982,5	MCF-7	breast:
11	chr2:85625848..85628085-chr2:85842277..85844956,2	MCF-7	breast:
12	chr2:85786982..85789648-chr2:85837896..85843296,4	MCF-7	breast:
13	chr2:85579163..85582551-chr2:85842255..85845885,4	K562	blood:
14	chr2:85644680..85648320-chr2:85841692..85845956,4	K562	blood:
15	chr2:85764765..85769369-chr2:85840508..85847982,10	K562	blood:
16	chr2:85555196..85556928-chr2:85841826..85844560,2	K562	blood:
17	chr2:85837207..85840832-chr2:85841070..85844212,15	K562	blood:

No data

Variant related genes	Relation type
USP39	TF binding region
C2orf68	TF binding region
ENSG00000115486	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000242125	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000168887	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1049359	1.00[EUR][1000 genomes]
rs11544042	1.00[EUR][1000 genomes]
rs17736515	0.83[EUR][1000 genomes]
rs2232739	0.91[EUR][1000 genomes]
rs41290037	0.91[EUR][1000 genomes]
rs55671524	0.83[EUR][1000 genomes]
rs55759724	0.91[EUR][1000 genomes]
rs56367745	0.87[EUR][1000 genomes]
rs57762218	1.00[ASN][1000 genomes]
rs59048598	1.00[ASN][1000 genomes]
rs60661938	1.00[ASN][1000 genomes]
rs60755293	1.00[ASN][1000 genomes]
rs61536745	1.00[ASN][1000 genomes]
rs72843878	1.00[EUR][1000 genomes]
rs72843879	0.91[EUR][1000 genomes]
rs72923039	1.00[ASN][1000 genomes]
rs7607181	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6547627	USP39	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85839600-85843200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:85839800-85843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:85839800-85843200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:85840000-85843200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:85842400-85843200	Flanking Active TSS	Dnd41	blood
6	chr2:85842400-85844400	Active TSS	GM12878-XiMat	blood
7	chr2:85842600-85843200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr2:85842600-85843200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr2:85842600-85843200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:85842600-85843200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:85842600-85843200	Flanking Active TSS	Stomach Mucosa	stomach
12	chr2:85842600-85844000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:85842600-85844000	Active TSS	Brain Cingulate Gyrus	brain
14	chr2:85842600-85844000	Active TSS	Fetal Lung	lung
15	chr2:85842600-85844000	Active TSS	Rectal Smooth Muscle	rectum
16	chr2:85842600-85844200	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr2:85842600-85844400	Active TSS	Brain Anterior Caudate	brain
18	chr2:85842600-85845000	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr2:85842800-85843200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr2:85842800-85843200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:85842800-85843200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:85842800-85843200	Flanking Active TSS	Fetal Muscle Trunk	muscle
23	chr2:85842800-85843200	Flanking Active TSS	Fetal Muscle Leg	muscle
24	chr2:85842800-85843200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr2:85842800-85843200	Weak transcription	Spleen	Spleen
26	chr2:85842800-85844000	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr2:85842800-85844000	Active TSS	Brain Germinal Matrix	brain
28	chr2:85842800-85844000	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr2:85842800-85844000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:85842800-85844000	Active TSS	Colonic Mucosa	Colon
31	chr2:85842800-85844000	Active TSS	Duodenum Mucosa	Duodenum
32	chr2:85842800-85844000	Active TSS	Pancreas	Pancrea
33	chr2:85842800-85844000	Active TSS	Stomach Smooth Muscle	stomach
34	chr2:85842800-85844000	Active TSS	K562	blood
35	chr2:85842800-85844000	Active TSS	Monocytes-CD14+_RO01746	blood
36	chr2:85842800-85844200	Active TSS	H1 Cell Line	embryonic stem cell
37	chr2:85842800-85844200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:85842800-85844200	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr2:85842800-85844200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:85842800-85844200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:85842800-85844200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:85842800-85844200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:85842800-85844200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:85842800-85844200	Active TSS	Esophagus	oesophagus
45	chr2:85842800-85844200	Active TSS	Fetal Brain Female	brain
46	chr2:85842800-85844200	Active TSS	Fetal Intestine Small	intestine
47	chr2:85842800-85844200	Active TSS	Fetal Kidney	kidney
48	chr2:85842800-85844200	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr2:85842800-85844200	Active TSS	Osteobl	bone
50	chr2:85842800-85844400	Active TSS	ES-I3 Cell Line	embryonic stem cell

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