Variant report

Variant	rs5030141
Chromosome Location	chr11:32455853-32455854
allele	A/C
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	chr11:32455696-32457733	PFSK-1	brain:	n/a	n/a
2	CTCF	chr11:32455847-32456630	A549	lung:	n/a	n/a
3	SUZ12	chr11:32453725-32461544	NT2-D1	testis:	n/a	n/a
4	BACH1	chr11:32455379-32455942	K562	blood:	n/a	n/a
5	JUN	chr11:32453532-32456818	K562	blood:	n/a	chr11:32453717-32453725
6	CTBP2	chr11:32454448-32456818	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:32455132-32457736	K562	blood:	n/a	n/a
8	POLR2A	chr11:32453940-32456452	K562	blood:	n/a	n/a
9	MAX	chr11:32454537-32457687	K562	blood:	n/a	chr11:32457467-32457477
10	MAX	chr11:32455170-32457723	K562	blood:	n/a	chr11:32457467-32457477
11	TAL1	chr11:32455399-32456659	K562	blood:	n/a	n/a
12	MYC	chr11:32455256-32457710	NB4	blood:	n/a	chr11:32457467-32457477
13	ZC3H11A	chr11:32455820-32456370	K562	blood:	n/a	n/a
14	POLR2A	chr11:32455724-32456537	K562	blood:	n/a	n/a
15	EGR1	chr11:32455713-32456655	K562	blood:	n/a	chr11:32455801-32455810
16	RCOR1	chr11:32454151-32456441	K562	blood:	n/a	n/a
17	HEY1	chr11:32455651-32456948	K562	blood:	n/a	chr11:32456092-32456107 chr11:32456933-32456948 chr11:32456201-32456216
18	TEAD4	chr11:32454979-32456457	K562	blood:	n/a	n/a
19	IRF1	chr11:32455262-32456419	K562	blood:	n/a	chr11:32455294-32455308
20	TAF1	chr11:32455834-32456477	PFSK-1	brain:	n/a	n/a
21	RCOR1	chr11:32455243-32455896	K562	blood:	n/a	n/a
22	MAX	chr11:32454143-32458628	NB4	blood:	n/a	chr11:32457467-32457477
23	MYC	chr11:32455104-32457646	K562	blood:	n/a	chr11:32457467-32457477
24	ZNF263	chr11:32455573-32457559	HEK293-T-REx	kidney:	n/a	chr11:32456089-32456098
25	JUND	chr11:32454141-32456484	K562	blood:	n/a	n/a
26	POLR2A	chr11:32453980-32457577	K562	blood:	n/a	n/a
27	CBX3	chr11:32455679-32456442	K562	blood:	n/a	n/a
28	REST	chr11:32455487-32456475	HL-60	blood:	n/a	chr11:32455640-32455647 chr11:32455796-32455816
29	ETS1	chr11:32455849-32456493	K562	blood:	n/a	chr11:32455949-32455962 chr11:32456103-32456113
30	ZMIZ1	chr11:32455324-32456379	K562	blood:	n/a	n/a
31	SIN3AK20	chr11:32455831-32456401	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr11:32455061-32456487	K562	blood:	n/a	n/a
33	SUZ12	chr11:32453771-32458890	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr11:32454161-32457678	K562	blood:	n/a	n/a
35	NR2F2	chr11:32455726-32456421	K562	blood:	n/a	n/a
36	POLR2A	chr11:32455366-32457646	HL-60	blood:	n/a	n/a
37	HEY1	chr11:32455141-32456962	K562	blood:	n/a	chr11:32456092-32456107 chr11:32456933-32456948 chr11:32456201-32456216
38	ZBTB7A	chr11:32455773-32456357	K562	blood:	n/a	chr11:32456221-32456230
39	TBP	chr11:32453973-32457616	K562	blood:	n/a	n/a
40	ZNF143	chr11:32455626-32456343	K562	blood:	n/a	n/a
41	BHLHE40	chr11:32455078-32456429	K562	blood:	n/a	n/a
42	POLR2A	chr11:32454208-32457616	K562	blood:	n/a	n/a
43	HMGN3	chr11:32454773-32457488	K562	blood:	n/a	n/a
44	POLR2A	chr11:32453512-32457942	NB4	blood:	n/a	n/a
45	JUN	chr11:32455809-32456408	K562	blood:	n/a	n/a
46	SPI1	chr11:32455461-32456536	HL-60	blood:	n/a	n/a
47	EGR1	chr11:32455631-32456335	K562	blood:	n/a	chr11:32455801-32455810
48	MYC	chr11:32454126-32457534	K562	blood:	n/a	chr11:32457467-32457477
49	REST	chr11:32455822-32456496	PFSK-1	brain:	n/a	n/a
50	POLR2A	chr11:32453842-32457744	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:32455369..32457971-chr11:32914210..32916339,2	K562	blood:
2	chr11:32455462..32457058-chr11:32608687..32611459,2	K562	blood:
3	chr11:32455134..32460391-chr11:32603988..32611641,10	K562	blood:
4	chr11:32455134..32458517-chr11:32603988..32607695,5	K562	blood:
5	chr11:32455544..32456179-chr21:40555264..40555769,2	NB4	blood:
6	chr11:32453512..32456485-chr11:32618384..32621260,2	K562	blood:

Variant related genes	Relation type
WT1	TF binding region
WT1-AS	TF binding region
ENSG00000149100	Chromatin interaction
ENSG00000060749	Chromatin interaction
ENSG00000183527	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10835913	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10835914	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10835915	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10835917	0.84[CHB][hapmap];0.93[CHD][hapmap]
rs11031778	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11031787	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11031788	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12575247	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569776	0.91[MEX][hapmap]
rs1799925	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234585	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2301250	0.83[CHD][hapmap]
rs2418910	0.83[CHD][hapmap]
rs2900741	0.85[CHD][hapmap]
rs2900753	0.82[EUR][1000 genomes]
rs34163689	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3809060	0.81[CHD][hapmap]
rs3809061	0.81[CHD][hapmap]
rs3858449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858451	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3930513	0.81[CHD][hapmap]
rs5030171	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5030277	0.86[MEX][hapmap]
rs5030280	0.86[MEX][hapmap]
rs5030281	0.86[MEX][hapmap]
rs59518979	0.85[EUR][1000 genomes]
rs61889255	0.85[EUR][1000 genomes]
rs61889256	0.84[EUR][1000 genomes]
rs7110547	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832108	chr11:32395937-32560583	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1044547	chr11:32435753-32465233	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2753303	chr11:32447324-32494924	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1051559	chr11:32447347-32465233	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5030141	MTMR4	trans	cerebellum	SCAN
rs5030141	CRYGA	trans	parietal	SCAN
rs5030141	PRR5L	cis	cerebellum	SCAN
rs5030141	CSTF3	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32450200-32457400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr11:32453400-32459600	Active TSS	Right Atrium	heart
3	chr11:32454400-32456200	Bivalent Enhancer	Liver	Liver
4	chr11:32454400-32456200	Bivalent/Poised TSS	Fetal Kidney	kidney
5	chr11:32454400-32456400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
6	chr11:32454600-32456400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:32454600-32456400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:32454600-32456600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr11:32454600-32456600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
10	chr11:32454600-32456800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
11	chr11:32454600-32457000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:32454600-32458600	Bivalent/Poised TSS	Left Ventricle	heart
13	chr11:32454600-32458800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
14	chr11:32454600-32459800	Active TSS	Ovary	ovary
15	chr11:32454800-32456000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
16	chr11:32454800-32456000	Enhancers	Gastric	stomach
17	chr11:32454800-32456000	Bivalent Enhancer	Stomach Mucosa	stomach
18	chr11:32454800-32456200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
19	chr11:32454800-32456200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr11:32454800-32456200	Bivalent/Poised TSS	Colonic Mucosa	Colon
21	chr11:32454800-32456200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
22	chr11:32454800-32456400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
23	chr11:32454800-32456400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
24	chr11:32454800-32456400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
25	chr11:32454800-32456600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:32454800-32456600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
27	chr11:32454800-32457800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:32454800-32457800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:32454800-32458200	Bivalent Enhancer	Esophagus	oesophagus
30	chr11:32454800-32458600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr11:32455000-32456000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
32	chr11:32455000-32457400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr11:32455000-32459400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
34	chr11:32455200-32456000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:32455200-32456000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:32455200-32456000	Flanking Active TSS	Spleen	Spleen
37	chr11:32455200-32456200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
38	chr11:32455200-32456200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
39	chr11:32455200-32456200	Bivalent Enhancer	Fetal Heart	heart
40	chr11:32455200-32456200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
41	chr11:32455200-32456600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
42	chr11:32455200-32456600	Bivalent Enhancer	Brain Germinal Matrix	brain
43	chr11:32455200-32457200	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr11:32455200-32458200	Enhancers	Pancreas	Pancrea
45	chr11:32455400-32456000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
46	chr11:32455400-32456000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
47	chr11:32455400-32456000	Bivalent Enhancer	HMEC	breast
48	chr11:32455400-32456200	Bivalent Enhancer	Brain Substantia Nigra	brain
49	chr11:32455400-32456400	Flanking Active TSS	Right Ventricle	heart
50	chr11:32455600-32456000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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