Variant report

Variant	rs1915943
Chromosome Location	chr3:150316954-150316955
allele	C/G
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	CHD1	chr3:150316297-150317049	GM12878	blood:	n/a	n/a
2	PML	chr3:150316132-150316983	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:150316374-150316980	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:150316259-150319258	GM12878	blood:	n/a	n/a
5	MTA3	chr3:150316205-150318380	GM12878	blood:	n/a	n/a
6	WRNIP1	chr3:150316282-150317151	GM12878	blood:	n/a	n/a
7	ZNF384	chr3:150316094-150316979	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:150316666-150317040	GM12892	blood:	n/a	n/a
9	EBF1	chr3:150316119-150317046	GM12878	blood:	n/a	chr3:150316693-150316704
10	CHD2	chr3:150316429-150316963	GM12878	blood:	n/a	n/a
11	RUNX3	chr3:150316808-150317225	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:150316345-150317049	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:150315973-150317993	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:150316310-150317106	Raji	blood:	n/a	n/a
15	POU2F2	chr3:150316240-150317025	GM12878	blood:	n/a	chr3:150316560-150316573
16	POLR2A	chr3:150316308-150317326	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:150316223-150317277	GM12878	blood:	n/a	n/a
18	STAT5A	chr3:150316667-150317118	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:150316658-150317272	GM12892	blood:	n/a	n/a
20	RUNX3	chr3:150316185-150317228	GM12878	blood:	n/a	n/a
21	RELA	chr3:150316321-150317899	GM12891	blood:	n/a	n/a
22	POLR2A	chr3:150316339-150317094	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150316261..150319464-chr3:150319733..150322939,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198843	TF binding region
ENSG00000120742	Chromatin interaction
ENSG00000198843	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1133494	0.86[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13071114	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13097283	0.94[CEU][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs14434	0.89[ASN][1000 genomes]
rs1464517	0.86[LWK][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1818788	1.00[ASN][1000 genomes]
rs1915942	1.00[ASN][1000 genomes]
rs2049229	0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2090916	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2204112	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2204113	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2868946	0.89[ASN][1000 genomes]
rs2868947	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440683	0.89[ASN][1000 genomes]
rs6790726	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6798173	1.00[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6801796	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7374917	0.89[ASN][1000 genomes]
rs7433606	1.00[CEU][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7628889	0.89[ASN][1000 genomes]
rs7631671	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7638500	0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7642917	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8052	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9289818	0.89[ASN][1000 genomes]
rs9289821	1.00[ASN][1000 genomes]
rs954068	0.81[ASN][1000 genomes]
rs9809820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9842446	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9865177	1.00[ASN][1000 genomes]
rs9874800	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1915943	TM4SF4	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150265600-150320600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:150265600-150320600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:150295600-150318600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:150301600-150320200	Weak transcription	Small Intestine	intestine
5	chr3:150302400-150320000	Weak transcription	Brain Germinal Matrix	brain
6	chr3:150303600-150317400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:150303600-150319200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:150303800-150317200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:150303800-150317400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:150303800-150318000	Weak transcription	NHLF	lung
11	chr3:150303800-150318800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:150303800-150318800	Weak transcription	Fetal Lung	lung
13	chr3:150303800-150320000	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:150303800-150320000	Weak transcription	Fetal Brain Female	brain
15	chr3:150303800-150320000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:150303800-150320800	Weak transcription	Lung	lung
17	chr3:150303800-150320800	Weak transcription	Spleen	Spleen
18	chr3:150304000-150320000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:150304000-150320000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:150304000-150320000	Weak transcription	Fetal Stomach	stomach
21	chr3:150304000-150320600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:150304400-150317600	Weak transcription	HepG2	liver
23	chr3:150304400-150320000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:150304400-150320200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:150304400-150320600	Weak transcription	Ovary	ovary
26	chr3:150304600-150318600	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:150304800-150320400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:150305000-150317000	Weak transcription	Right Atrium	heart
29	chr3:150305000-150318400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:150305200-150317600	Weak transcription	A549	lung
31	chr3:150306200-150318000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:150306200-150320000	Weak transcription	Left Ventricle	heart
33	chr3:150306400-150317200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:150306400-150318200	Weak transcription	Primary T cells from cord blood	blood
35	chr3:150306400-150319000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr3:150306600-150317000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:150307200-150317800	Weak transcription	Dnd41	blood
38	chr3:150312800-150320000	Weak transcription	Fetal Intestine Small	intestine
39	chr3:150314000-150318000	Weak transcription	Pancreas	Pancrea
40	chr3:150314800-150317800	Weak transcription	Psoas Muscle	Psoas
41	chr3:150315200-150317000	Enhancers	NHEK	skin
42	chr3:150315200-150317400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:150315600-150317600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr3:150315600-150318000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr3:150315600-150319000	Enhancers	Primary B cells from peripheral blood	blood
46	chr3:150315600-150319200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:150315600-150320000	Enhancers	HMEC	breast
48	chr3:150315800-150317800	Enhancers	Primary B cells from cord blood	blood
49	chr3:150316200-150317200	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr3:150316200-150317200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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