Variant report

Variant	rs11544042
Chromosome Location	chr2:85843348-85843349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr2:85843082-85843409	Hela-S3	cervix:	n/a	n/a
2	TAF1	chr2:85843062-85843772	ECC-1	luminal epithelium:	n/a	n/a
3	CREB1	chr2:85842993-85843725	A549	lung:	n/a	n/a
4	NR2F2	chr2:85843041-85843553	K562	blood:	n/a	n/a
5	CCNT2	chr2:85843089-85843649	K562	blood:	n/a	n/a
6	SIN3AK20	chr2:85843035-85843532	H1-hESC	embryonic stem cell:	n/a	n/a
7	NRF1	chr2:85843107-85843508	H1-hESC	embryonic stem cell:	n/a	chr2:85843283-85843294 chr2:85843284-85843298
8	MAZ	chr2:85843014-85843726	K562	blood:	n/a	n/a
9	POLR2A	chr2:85842992-85843746	U87	brain:	n/a	n/a
10	PBX3	chr2:85842999-85843596	A549	lung:	n/a	chr2:85843249-85843258
11	REST	chr2:85842971-85843708	HL-60	blood:	n/a	n/a
12	TCF12	chr2:85843123-85843601	GM12878	blood:	n/a	n/a
13	YY1	chr2:85843000-85843639	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:85842936-85843713	GM12891	blood:	n/a	n/a
15	UBTF	chr2:85843051-85843689	K562	blood:	n/a	n/a
16	GABPA	chr2:85842973-85843540	MCF-7	breast:	n/a	chr2:85843284-85843298
17	POLR2A	chr2:85842962-85843608	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr2:85842938-85843589	HEK293	kidney:	n/a	n/a
19	MAZ	chr2:85843052-85843545	GM12878	blood:	n/a	n/a
20	ETS1	chr2:85843033-85843569	GM12878	blood:	n/a	chr2:85843141-85843156 chr2:85843143-85843156
21	E2F6	chr2:85843049-85843756	K562	blood:	n/a	chr2:85843356-85843367 chr2:85843625-85843642 chr2:85843285-85843294
22	NFYA	chr2:85843105-85843403	Hela-S3	cervix:	n/a	chr2:85843242-85843260
23	POLR2A	chr2:85843181-85843698	IMR90	lung:	n/a	n/a
24	NR2F2	chr2:85842991-85843603	MCF-7	breast:	n/a	n/a
25	FOXM1	chr2:85842936-85843461	GM12878	blood:	n/a	n/a
26	SP4	chr2:85842948-85843654	H1-hESC	embryonic stem cell:	n/a	n/a
27	HDAC2	chr2:85842974-85843532	HepG2	liver:	n/a	chr2:85843265-85843274
28	ATF2	chr2:85842984-85843376	GM12878	blood:	n/a	n/a
29	YY1	chr2:85842947-85843722	HepG2	liver:	n/a	chr2:85843683-85843694
30	CTCF	chr2:85843200-85843350	HepG2	liver:	n/a	n/a
31	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
32	GATA3	chr2:85842933-85843766	A549	lung:	n/a	n/a
33	POLR2A	chr2:85842986-85843873	GM12878	blood:	n/a	n/a
34	EGR1	chr2:85843051-85843435	K562	blood:	n/a	chr2:85843168-85843175 chr2:85843285-85843294
35	POLR2A	chr2:85842928-85843658	K562	blood:	n/a	n/a
36	POLR2A	chr2:85842806-85843710	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr2:85843058-85843652	HUVEC	blood vessel:	n/a	n/a
38	TAF7	chr2:85843080-85843652	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr2:85843220-85843370	HMEC	breast:	n/a	n/a
40	CTCF	chr2:85843220-85843370	GM12869	blood:	n/a	n/a
41	CEBPD	chr2:85843138-85843601	K562	blood:	n/a	n/a
42	ELF1	chr2:85843015-85843696	MCF-7	breast:	n/a	n/a
43	SIN3AK20	chr2:85843045-85843630	HepG2	liver:	n/a	n/a
44	POLR2A	chr2:85843013-85843809	HL-60	blood:	n/a	n/a
45	SIN3AK20	chr2:85843246-85843446	SK-N-SH	brain:	n/a	n/a
46	NANOG	chr2:85843094-85843424	H1-hESC	embryonic stem cell:	n/a	n/a
47	RCOR1	chr2:85843061-85843517	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr2:85842956-85843720	ECC-1	luminal epithelium:	n/a	n/a
49	MXI1	chr2:85843095-85843583	Hela-S3	cervix:	n/a	n/a
50	USF1	chr2:85843082-85843376	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:85581050..85582551-chr2:85842255..85845112,2	K562	blood:
2	chr2:85843134..85843800-chr6:36561705..36562333,2	Hela-S3	cervix:
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	chr2:85579163..85582551-chr2:85842255..85845885,4	K562	blood:
13	chr2:85843328..85843837-chr7:65579492..65580235,2	Hela-S3	cervix:
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:

Variant related genes	Relation type
C2orf68	TF binding region
USP39	TF binding region
ENSG00000180198	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000115459	Chromatin interaction
ENSG00000241258	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000042445	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000242125	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1049359	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17736515	0.86[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2232739	0.88[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];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]
rs6547627	1.00[EUR][1000 genomes]
rs72843878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72843879	0.91[EUR][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
rs11544042	USP39	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85842400-85844400	Active TSS	GM12878-XiMat	blood
2	chr2:85842600-85844000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:85842600-85844000	Active TSS	Brain Cingulate Gyrus	brain
4	chr2:85842600-85844000	Active TSS	Fetal Lung	lung
5	chr2:85842600-85844000	Active TSS	Rectal Smooth Muscle	rectum
6	chr2:85842600-85844200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr2:85842600-85844400	Active TSS	Brain Anterior Caudate	brain
8	chr2:85842600-85845000	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr2:85842800-85844000	Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr2:85842800-85844000	Active TSS	Brain Germinal Matrix	brain
11	chr2:85842800-85844000	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr2:85842800-85844000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:85842800-85844000	Active TSS	Colonic Mucosa	Colon
14	chr2:85842800-85844000	Active TSS	Duodenum Mucosa	Duodenum
15	chr2:85842800-85844000	Active TSS	Pancreas	Pancrea
16	chr2:85842800-85844000	Active TSS	Stomach Smooth Muscle	stomach
17	chr2:85842800-85844000	Active TSS	K562	blood
18	chr2:85842800-85844000	Active TSS	Monocytes-CD14+_RO01746	blood
19	chr2:85842800-85844200	Active TSS	H1 Cell Line	embryonic stem cell
20	chr2:85842800-85844200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:85842800-85844200	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr2:85842800-85844200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:85842800-85844200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:85842800-85844200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:85842800-85844200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:85842800-85844200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:85842800-85844200	Active TSS	Esophagus	oesophagus
28	chr2:85842800-85844200	Active TSS	Fetal Brain Female	brain
29	chr2:85842800-85844200	Active TSS	Fetal Intestine Small	intestine
30	chr2:85842800-85844200	Active TSS	Fetal Kidney	kidney
31	chr2:85842800-85844200	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr2:85842800-85844200	Active TSS	Osteobl	bone
33	chr2:85842800-85844400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr2:85842800-85844400	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr2:85842800-85844400	Active TSS	Brain Angular Gyrus	brain
36	chr2:85842800-85844600	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr2:85842800-85844600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:85842800-85844800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:85843000-85843400	Active TSS	Primary hematopoietic stem cells	blood
40	chr2:85843000-85843600	Enhancers	Fetal Brain Male	brain
41	chr2:85843000-85843800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr2:85843000-85843800	Active TSS	Primary B cells from cord blood	blood
43	chr2:85843000-85843800	Active TSS	Adipose Nuclei	Adipose
44	chr2:85843000-85843800	Active TSS	Fetal Heart	heart
45	chr2:85843000-85843800	Active TSS	Placenta Amnion	Placenta Amnion
46	chr2:85843000-85844000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:85843000-85844000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:85843000-85844000	Active TSS	Primary T cells from cord blood	blood
49	chr2:85843000-85844000	Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr2:85843000-85844000	Active TSS	Liver	Liver

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