Variant report

Variant	rs7322038
Chromosome Location	chr13:30510224-30510225
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	PML	chr13:30509566-30510290	GM12878	blood:	n/a	n/a
2	MEF2A	chr13:30509585-30510258	GM12878	blood:	n/a	chr13:30510067-30510088 chr13:30510071-30510086 chr13:30510074-30510083 chr13:30510067-30510088 chr13:30510071-30510087 chr13:30510067-30510088 chr13:30510072-30510087 chr13:30510072-30510086 chr13:30510073-30510084
3	RCOR1	chr13:30509766-30510358	GM12878	blood:	n/a	n/a
4	FOXM1	chr13:30509511-30510274	GM12878	blood:	n/a	n/a
5	BCLAF1	chr13:30509578-30510246	GM12878	blood:	n/a	n/a
6	MEF2C	chr13:30509715-30510298	GM12878	blood:	n/a	chr13:30510067-30510088 chr13:30510071-30510086 chr13:30510074-30510083 chr13:30510067-30510088 chr13:30510071-30510087 chr13:30510067-30510088 chr13:30510072-30510087 chr13:30510072-30510086 chr13:30510073-30510084
7	TCF12	chr13:30510140-30510482	GM12878	blood:	n/a	chr13:30510247-30510257 chr13:30510401-30510408
8	CHD2	chr13:30509662-30510348	GM12878	blood:	n/a	n/a
9	SPI1	chr13:30509665-30510491	HL-60	blood:	n/a	n/a
10	MAZ	chr13:30509696-30510328	GM12878	blood:	n/a	n/a
11	TCF3	chr13:30509620-30510558	GM12878	blood:	n/a	chr13:30509889-30509904 chr13:30509698-30509711 chr13:30509892-30509901
12	MAX	chr13:30510138-30510505	H1-hESC	embryonic stem cell:	n/a	n/a
13	MTA3	chr13:30509549-30510491	GM12878	blood:	n/a	n/a
14	ATF2	chr13:30509557-30510249	GM12878	blood:	n/a	n/a
15	FOXM1	chr13:30509632-30510232	GM12878	blood:	n/a	n/a
16	IKZF1	chr13:30509557-30510246	GM12878	blood:	n/a	n/a
17	NFATC1	chr13:30509599-30510252	GM12878	blood:	n/a	n/a
18	ZEB1	chr13:30509608-30510519	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30508008..30510755-chr13:30510923..30512750,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-90M5.1.1-1	chr13:30510042-30510361	ENSG00000122043.6

Variant related genes	Relation type
LINC00544	TF binding region
ENSG00000122043	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1093631	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1325368	0.84[ASN][1000 genomes]
rs17631642	0.84[ASN][1000 genomes]
rs17688104	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs3843677	0.88[ASN][1000 genomes]
rs3843678	0.85[ASN][1000 genomes]
rs4318068	0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4769779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4769780	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4769781	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585668	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634413	0.82[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs646917	0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7319246	0.87[ASN][1000 genomes]
rs7320271	0.87[ASN][1000 genomes]
rs7320355	0.87[ASN][1000 genomes]
rs7320728	0.87[ASN][1000 genomes]
rs7339208	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs74042894	0.87[ASN][1000 genomes]
rs7992473	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs7994222	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs843883	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912788	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs927731	0.84[ASN][1000 genomes]
rs927732	0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs927733	0.82[ASN][1000 genomes]
rs9314990	0.87[MEX][hapmap];0.81[AMR][1000 genomes]
rs9314991	0.87[LWK][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9506244	0.87[LWK][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9508594	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7322038	SH3BGRL2	trans	cerebellum	SCAN
rs7322038	MTIF3	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30498800-30513200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:30508600-30510400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr13:30508800-30510600	Enhancers	Fetal Brain Male	brain
4	chr13:30509000-30510800	Enhancers	Stomach Mucosa	stomach
5	chr13:30509000-30512600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr13:30509200-30510400	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr13:30509200-30510600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:30509200-30511000	Enhancers	Primary B cells from peripheral blood	blood
9	chr13:30509400-30510400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr13:30509400-30510400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr13:30509400-30510600	Enhancers	Fetal Intestine Large	intestine
12	chr13:30509400-30510600	Flanking Active TSS	GM12878-XiMat	blood
13	chr13:30509400-30510800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:30509400-30511600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:30509400-30511600	Enhancers	Liver	Liver
16	chr13:30509400-30512800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr13:30509600-30510400	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr13:30509600-30510600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:30509600-30510800	Enhancers	Brain Hippocampus Middle	brain
20	chr13:30509600-30510800	Enhancers	Fetal Intestine Small	intestine
21	chr13:30509600-30511000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr13:30509600-30511200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr13:30509800-30510400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr13:30509800-30510400	Enhancers	Lung	lung
25	chr13:30509800-30510600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr13:30509800-30510600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr13:30509800-30510600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr13:30509800-30510600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr13:30509800-30510600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr13:30509800-30510800	Enhancers	Primary hematopoietic stem cells	blood
31	chr13:30509800-30510800	Enhancers	Pancreas	Pancrea
32	chr13:30509800-30510800	Enhancers	Spleen	Spleen
33	chr13:30509800-30511000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr13:30509800-30511000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr13:30509800-30515000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr13:30510000-30510400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr13:30510000-30510600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
38	chr13:30510000-30510600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr13:30510000-30510600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
40	chr13:30510000-30510600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr13:30510000-30510600	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr13:30510000-30510600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr13:30510000-30510600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr13:30510000-30510600	Active TSS	Brain Anterior Caudate	brain
45	chr13:30510000-30510600	Flanking Active TSS	Fetal Thymus	thymus
46	chr13:30510000-30510600	Flanking Active TSS	Thymus	Thymus
47	chr13:30510000-30510800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr13:30510000-30511000	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr13:30510000-30511000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr13:30510000-30511000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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