Variant report

Variant	rs12103533
Chromosome Location	chr17:38336816-38336817
allele	A/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	BRCA1	chr17:38336430-38337016	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr17:38336196-38337038	U87	brain:	n/a	n/a
3	POLR2A	chr17:38336612-38337576	PFSK-1	brain:	n/a	n/a
4	GATA3	chr17:38336776-38337537	MCF-7	breast:	n/a	chr17:38337019-38337027
5	EGR1	chr17:38336616-38336845	K562	blood:	n/a	n/a
6	SMARCC1	chr17:38335978-38336941	Hela-S3	cervix:	n/a	n/a
7	ESR1	chr17:38336338-38336888	ECC-1	luminal epithelium:	n/a	n/a
8	TFAP2A	chr17:38336301-38337247	Hela-S3	cervix:	n/a	chr17:38336842-38336852 chr17:38336842-38336852 chr17:38336842-38336852 chr17:38336840-38336854 chr17:38336840-38336854 chr17:38336842-38336852
9	FOXM1	chr17:38336805-38337612	MCF-7	breast:	n/a	n/a
10	POLR2A	chr17:38336007-38338028	MCF-7	breast:	n/a	n/a
11	SIN3AK20	chr17:38336767-38337550	MCF-7	breast:	n/a	n/a
12	NR2F2	chr17:38336789-38337486	MCF-7	breast:	n/a	n/a
13	ESR1	chr17:38336454-38336816	T-47D	breast:	n/a	n/a
14	EGR1	chr17:38336590-38336820	K562	blood:	n/a	n/a
15	MAZ	chr17:38335888-38336816	IMR90	lung:	n/a	chr17:38336059-38336069 chr17:38336455-38336464 chr17:38336127-38336136
16	TCF12	chr17:38336697-38337611	MCF-7	breast:	n/a	chr17:38337105-38337112
17	TFAP2C	chr17:38336030-38337319	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38274376..38281367-chr17:38331383..38338006,23	MCF-7	breast:
2	chr17:38331383..38339312-chr17:38470464..38480799,28	MCF-7	breast:
3	chr17:38336790..38337483-chr17:38478299..38479085,2	MCF-7	breast:
4	chr17:38295337..38298287-chr17:38335911..38338281,4	MCF-7	breast:
5	chr17:38335151..38337068-chr17:38457907..38459512,2	MCF-7	breast:
6	chr17:38331368..38338782-chr17:38460574..38470405,11	MCF-7	breast:
7	chr17:38295337..38297025-chr17:38334277..38336904,2	K562	blood:
8	chr17:38335879..38338134-chr17:38374200..38376894,2	MCF-7	breast:
9	chr17:38136752..38138945-chr17:38335315..38337237,2	MCF-7	breast:
10	chr17:38336165..38338939-chr17:38598006..38600043,2	MCF-7	breast:

Variant related genes	Relation type
RAPGEFL1	TF binding region
ENSG00000108344	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000270145	Chromatin interaction
ENSG00000171475	Chromatin interaction
ENSG00000108349	Chromatin interaction
ENSG00000141753	Chromatin interaction
ENSG00000188895	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10451257	1.00[TSI][hapmap]
rs10512482	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1104761	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11540720	1.00[EUR][1000 genomes]
rs15685	0.92[EUR][1000 genomes]
rs16965660	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16965669	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965734	1.00[EUR][1000 genomes]
rs16965736	1.00[EUR][1000 genomes]
rs16965748	1.00[EUR][1000 genomes]
rs16965774	1.00[EUR][1000 genomes]
rs16965778	1.00[EUR][1000 genomes]
rs17616543	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17616672	0.92[EUR][1000 genomes]
rs17616879	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17617263	0.92[EUR][1000 genomes]
rs17678817	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17678959	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17678990	0.92[EUR][1000 genomes]
rs17679086	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17679361	0.92[EUR][1000 genomes]
rs17680217	0.92[EUR][1000 genomes]
rs17680410	0.92[EUR][1000 genomes]
rs17680507	0.92[EUR][1000 genomes]
rs17680624	0.92[EUR][1000 genomes]
rs2012667	0.92[EUR][1000 genomes]
rs2229773	0.92[EUR][1000 genomes]
rs28362320	1.00[EUR][1000 genomes]
rs28362321	0.92[EUR][1000 genomes]
rs28526298	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs33998939	0.92[EUR][1000 genomes]
rs34270904	1.00[EUR][1000 genomes]
rs34300454	1.00[EUR][1000 genomes]
rs35783632	0.92[EUR][1000 genomes]
rs35898909	0.92[EUR][1000 genomes]
rs41283417	1.00[EUR][1000 genomes]
rs41283423	0.92[EUR][1000 genomes]
rs4134993	0.92[EUR][1000 genomes]
rs4134998	0.92[EUR][1000 genomes]
rs4135005	0.92[EUR][1000 genomes]
rs4135007	0.92[EUR][1000 genomes]
rs4135012	0.92[EUR][1000 genomes]
rs4135019	0.92[EUR][1000 genomes]
rs4135021	0.92[EUR][1000 genomes]
rs4135027	0.92[EUR][1000 genomes]
rs4135030	0.92[EUR][1000 genomes]
rs45612441	0.92[EUR][1000 genomes]
rs8067519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8071687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8077482	1.00[EUR][1000 genomes]
rs9889905	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9891944	0.92[EUR][1000 genomes]
rs9894364	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9894807	1.00[CEU][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9898500	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9899425	1.00[EUR][1000 genomes]
rs9900154	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9903293	1.00[EUR][1000 genomes]
rs9906274	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9909777	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9909811	1.00[CEU][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9910373	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9915775	1.00[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	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv525796	chr17:38306365-38405037	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12103533	RAPGEFL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38331400-38338200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr17:38333200-38347000	Weak transcription	Brain Substantia Nigra	brain
3	chr17:38333600-38337400	Active TSS	Esophagus	oesophagus
4	chr17:38333600-38339000	Weak transcription	Left Ventricle	heart
5	chr17:38333600-38339800	Weak transcription	Primary T cells from cord blood	blood
6	chr17:38333600-38347000	Weak transcription	Fetal Lung	lung
7	chr17:38334000-38337200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr17:38334000-38341400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:38334000-38347000	Weak transcription	HUVEC	blood vessel
10	chr17:38334200-38337400	Weak transcription	Adipose Nuclei	Adipose
11	chr17:38334200-38346800	Weak transcription	Spleen	Spleen
12	chr17:38334200-38347000	Weak transcription	GM12878-XiMat	blood
13	chr17:38334200-38347400	Weak transcription	Aorta	Aorta
14	chr17:38334400-38337600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr17:38334400-38346800	Weak transcription	Colon Smooth Muscle	Colon
16	chr17:38334400-38346800	Weak transcription	Ovary	ovary
17	chr17:38334600-38337600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:38334600-38339800	Enhancers	Fetal Muscle Leg	muscle
19	chr17:38334600-38345200	Weak transcription	Right Ventricle	heart
20	chr17:38334600-38346600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr17:38334600-38346800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr17:38334800-38337200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr17:38334800-38337400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:38335000-38337000	Weak transcription	Lung	lung
25	chr17:38335000-38337800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:38335000-38345000	Weak transcription	Brain Germinal Matrix	brain
27	chr17:38335000-38345400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr17:38335000-38346400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr17:38335200-38337000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:38335200-38337000	Weak transcription	Gastric	stomach
31	chr17:38335200-38337200	Weak transcription	Fetal Thymus	thymus
32	chr17:38335200-38337600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:38335200-38337600	Weak transcription	Brain Hippocampus Middle	brain
34	chr17:38335200-38338000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr17:38335200-38338200	Enhancers	Fetal Intestine Large	intestine
36	chr17:38335200-38338200	Genic enhancers	Fetal Intestine Small	intestine
37	chr17:38335200-38340400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr17:38335200-38346600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr17:38335200-38346800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:38335200-38346800	Weak transcription	Thymus	Thymus
41	chr17:38335200-38347000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:38335200-38347800	Weak transcription	Small Intestine	intestine
43	chr17:38335400-38340400	Weak transcription	Fetal Brain Female	brain
44	chr17:38335400-38346800	Weak transcription	Fetal Brain Male	brain
45	chr17:38335400-38347000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr17:38335600-38337200	Enhancers	NH-A	brain
47	chr17:38335800-38337000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr17:38335800-38337000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:38335800-38337000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr17:38335800-38337000	Enhancers	HSMM	muscle

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