Variant report

Variant	rs10188586
Chromosome Location	chr2:37311339-37311340
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	POLR2A	chr2:37310981-37312286	SK-N-SH	brain:	n/a	n/a
2	SIN3AK20	chr2:37310721-37312125	MCF-7	breast:	n/a	n/a
3	REST	chr2:37311048-37312065	A549	lung:	n/a	n/a
4	MAX	chr2:37310787-37312103	HepG2	liver:	n/a	n/a
5	MXI1	chr2:37310017-37312964	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr2:37310961-37311955	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr2:37311026-37311939	GM18951	blood:	n/a	n/a
8	MTA3	chr2:37310887-37312337	GM12878	blood:	n/a	n/a
9	EP300	chr2:37311143-37312023	A549	lung:	n/a	chr2:37311632-37311639
10	POLR2A	chr2:37310950-37312000	K562	blood:	n/a	n/a
11	POLR2A	chr2:37311106-37311953	GM19099	blood:	n/a	n/a
12	HMGN3	chr2:37310971-37311850	K562	blood:	n/a	n/a
13	MAX	chr2:37310921-37312085	Hela-S3	cervix:	n/a	n/a
14	TAF1	chr2:37310997-37311992	ECC-1	luminal epithelium:	n/a	n/a
15	ETS1	chr2:37310907-37311597	K562	blood:	n/a	n/a
16	CEBPB	chr2:37311224-37311941	K562	blood:	n/a	n/a
17	TAF1	chr2:37311311-37311807	SK-N-SH	brain:	n/a	n/a
18	E2F4	chr2:37311135-37311796	MCF10A-Er-Src	breast:	n/a	chr2:37311544-37311553 chr2:37311520-37311529 chr2:37311657-37311666
19	MXI1	chr2:37310996-37312045	K562	blood:	n/a	n/a
20	RUNX3	chr2:37310825-37312188	GM12878	blood:	n/a	n/a
21	TAF1	chr2:37311334-37311839	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr2:37310844-37311947	K562	blood:	n/a	n/a
23	MYC	chr2:37310984-37311900	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr2:37311119-37311954	HUVEC	blood vessel:	n/a	n/a
25	FOXM1	chr2:37310907-37311623	GM12878	blood:	n/a	n/a
26	SIN3AK20	chr2:37310912-37312096	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr2:37311160-37311885	HCT-116	colon:	n/a	n/a
28	ATF2	chr2:37311016-37311844	GM12878	blood:	n/a	n/a
29	HEY1	chr2:37311232-37311808	HepG2	liver:	n/a	n/a
30	MAX	chr2:37310910-37311809	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr2:37310882-37311908	GM12878	blood:	n/a	n/a
32	SMARCB1	chr2:37310942-37311959	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr2:37311091-37311975	Gliobla	brain:	n/a	n/a
34	TAF1	chr2:37311279-37311517	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr2:37310894-37311944	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr2:37311069-37312146	HepG2	liver:	n/a	n/a
37	TEAD4	chr2:37310903-37311464	H1-hESC	embryonic stem cell:	n/a	n/a
38	EGR1	chr2:37311301-37311924	K562	blood:	n/a	chr2:37311520-37311529 chr2:37311657-37311666 chr2:37311544-37311553 chr2:37311375-37311384
39	YY1	chr2:37310911-37311918	GM12878	blood:	n/a	chr2:37311766-37311780
40	ETS1	chr2:37310904-37311853	K562	blood:	n/a	chr2:37311632-37311642 chr2:37311620-37311633
41	POLR2A	chr2:37311223-37312091	K562	blood:	n/a	n/a
42	CEBPB	chr2:37311287-37311739	H1-hESC	embryonic stem cell:	n/a	n/a
43	TEAD4	chr2:37310940-37311611	H1-hESC	embryonic stem cell:	n/a	n/a
44	SIN3A	chr2:37310818-37311975	GM12878	blood:	n/a	n/a
45	MAZ	chr2:37310987-37312111	Hela-S3	cervix:	n/a	n/a
46	TBP	chr2:37311006-37311897	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr2:37311125-37311970	ECC-1	luminal epithelium:	n/a	n/a
48	CBX3	chr2:37310899-37312321	K562	blood:	n/a	n/a
49	GABPA	chr2:37311217-37311931	K562	blood:	n/a	chr2:37311521-37311530 chr2:37311656-37311670 chr2:37311656-37311667 chr2:37311658-37311667 chr2:37311543-37311554 chr2:37311519-37311530 chr2:37311543-37311552 chr2:37311543-37311557 chr2:37311653-37311667 chr2:37311519-37311533 chr2:37311656-37311665 chr2:37311540-37311554
50	MXI1	chr2:37310844-37312218	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:37192443..37195662-chr2:37309226..37313144,4	K562	blood:
2	chr2:37303145..37307773-chr2:37309967..37312516,4	MCF-7	breast:
3	chr2:37311074..37311574-chr7:100026079..100026796,2	Hela-S3	cervix:
4	chr2:37311131..37313325-chr2:37314182..37316886,3	MCF-7	breast:
5	chr2:37310057..37313374-chr2:37313742..37317078,6	K562	blood:

Variant related genes	Relation type
GPATCH11	TF binding region
ENSG00000152133	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000115808	Chromatin interaction
ENSG00000008869	Chromatin interaction

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

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

rs_ID	r²[population]
rs10176233	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs10176303	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10191403	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10194972	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12465097	0.97[AFR][1000 genomes]
rs12469391	0.97[AFR][1000 genomes]
rs13398187	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs13425846	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17020185	0.80[YRI][hapmap]
rs2307483	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs2373114	0.87[CEU][hapmap]
rs2541001	0.95[EUR][1000 genomes]
rs3845782	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs4648202	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs6718647	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6732075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7596489	1.00[CEU][hapmap];0.98[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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10188586	CCDC75	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37308800-37313200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:37310000-37311400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr2:37310200-37312400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:37310200-37313000	Active TSS	Right Atrium	heart
5	chr2:37310400-37312000	Active TSS	Brain Cingulate Gyrus	brain
6	chr2:37310400-37312000	Active TSS	Pancreas	Pancrea
7	chr2:37310400-37312200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:37310400-37312400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr2:37310400-37312400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:37310400-37312600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:37310400-37312600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr2:37310400-37312600	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr2:37310400-37312600	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr2:37310400-37312600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:37310400-37312600	Active TSS	GM12878-XiMat	blood
16	chr2:37310600-37311800	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr2:37310600-37312000	Active TSS	H1 Cell Line	embryonic stem cell
18	chr2:37310600-37312000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:37310600-37312000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:37310600-37312000	Active TSS	Brain Angular Gyrus	brain
21	chr2:37310600-37312000	Active TSS	Brain Anterior Caudate	brain
22	chr2:37310600-37312000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:37310600-37312000	Active TSS	Fetal Heart	heart
24	chr2:37310600-37312000	Active TSS	Fetal Intestine Small	intestine
25	chr2:37310600-37312000	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr2:37310600-37312000	Active TSS	Stomach Smooth Muscle	stomach
27	chr2:37310600-37312000	Active TSS	HMEC	breast
28	chr2:37310600-37312000	Active TSS	HSMM	muscle
29	chr2:37310600-37312000	Active TSS	HSMMtube	muscle
30	chr2:37310600-37312000	Active TSS	NHLF	lung
31	chr2:37310600-37312200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:37310600-37312200	Active TSS	Primary B cells from peripheral blood	blood
33	chr2:37310600-37312200	Active TSS	Primary T cells fromperipheralblood	blood
34	chr2:37310600-37312200	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr2:37310600-37312200	Active TSS	Fetal Brain Female	brain
36	chr2:37310600-37312200	Active TSS	Fetal Intestine Large	intestine
37	chr2:37310600-37312200	Active TSS	Fetal Kidney	kidney
38	chr2:37310600-37312200	Active TSS	Fetal Lung	lung
39	chr2:37310600-37312200	Active TSS	Fetal Muscle Leg	muscle
40	chr2:37310600-37312200	Active TSS	Fetal Thymus	thymus
41	chr2:37310600-37312200	Active TSS	NHDF-Ad	bronchial
42	chr2:37310600-37312400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:37310600-37312400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:37310600-37312400	Active TSS	Aorta	Aorta
45	chr2:37310600-37312400	Active TSS	Colonic Mucosa	Colon
46	chr2:37310600-37312400	Active TSS	Fetal Muscle Trunk	muscle
47	chr2:37310600-37312400	Active TSS	Fetal Stomach	stomach
48	chr2:37310600-37312400	Active TSS	Right Ventricle	heart
49	chr2:37310600-37312400	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr2:37310600-37312400	Active TSS	A549	lung

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