Variant report

Variant	rs17651941
Chromosome Location	chr15:52948626-52948627
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	GATA3	chr15:52948600-52948946	MCF-7	breast:	n/a	n/a
2	TCF7L2	chr15:52948585-52948946	MCF-7	breast:	n/a	n/a
3	FOXA1	chr15:52948489-52949077	A549	lung:	n/a	n/a
4	NR2F2	chr15:52948481-52948967	MCF-7	breast:	n/a	n/a
5	NR3C1	chr15:52948588-52948967	A549	lung:	n/a	chr15:52948810-52948824 chr15:52948804-52948830 chr15:52948804-52948830 chr15:52948804-52948830 chr15:52948804-52948830 chr15:52948809-52948826
6	FOXA1	chr15:52948564-52948996	A549	lung:	n/a	n/a
7	ESR1	chr15:52948518-52948892	T-47D	breast:	n/a	chr15:52948744-52948761
8	FOXM1	chr15:52948500-52949067	MCF-7	breast:	n/a	n/a
9	EP300	chr15:52948466-52949039	MCF-7	breast:	n/a	chr15:52948729-52948743
10	ESR1	chr15:52948473-52948971	T-47D	breast:	n/a	chr15:52948744-52948761
11	GATA3	chr15:52948369-52949283	MCF-7	breast:	n/a	n/a
12	ESR1	chr15:52948609-52948905	T-47D	breast:	n/a	chr15:52948744-52948761
13	JUND	chr15:52948548-52949086	T-47D	breast:	n/a	n/a
14	ESR1	chr15:52948552-52948905	T-47D	breast:	n/a	chr15:52948744-52948761
15	ESR1	chr15:52948523-52948993	T-47D	breast:	n/a	chr15:52948744-52948761
16	GATA3	chr15:52948465-52949170	MCF-7	breast:	n/a	n/a
17	GATA3	chr15:52948581-52948957	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52946056..52948651-chr15:52958978..52960779,2	MCF-7	breast:
2	chr15:52943691..52945442-chr15:52947121..52948885,2	MCF-7	breast:
3	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:

Variant related genes	Relation type
FAM214A	TF binding region
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11070906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11631979	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11633933	0.95[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs12594964	0.82[EUR][1000 genomes]
rs13329393	0.81[CEU][hapmap]
rs2414160	0.81[CEU][hapmap]
rs2899492	0.82[EUR][1000 genomes]
rs55895733	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167494	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs73396766	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73396785	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8030141	0.85[CEU][hapmap]
rs8030871	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8036979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv457140	chr15:52901433-52968746	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking 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
5	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17651941	Hs.11898	cis	multi-tissue	Pritchard
rs17651941	KIAA1370	cis	uninvolved skin	skin_eQTL
rs17651941	KIAA1370	cis	Lymphoblastoid	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr15:52904000-52956800	Weak transcription	Esophagus	oesophagus
3	chr15:52908600-52956200	Weak transcription	Gastric	stomach
4	chr15:52909600-52950800	Weak transcription	Pancreas	Pancrea
5	chr15:52927800-52958600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:52928000-52955200	Weak transcription	Thymus	Thymus
7	chr15:52928000-52956400	Weak transcription	Lung	lung
8	chr15:52944200-52951800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr15:52944200-52965800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:52944400-52950000	Weak transcription	Ovary	ovary
11	chr15:52944400-52950400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:52944400-52951000	Weak transcription	Fetal Stomach	stomach
13	chr15:52944400-52957000	Weak transcription	Brain Germinal Matrix	brain
14	chr15:52944400-52969600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:52944400-52970200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:52944600-52949600	Weak transcription	Fetal Brain Female	brain
17	chr15:52944600-52950000	Enhancers	Liver	Liver
18	chr15:52944600-52962000	Weak transcription	Aorta	Aorta
19	chr15:52944600-52965000	Strong transcription	Primary B cells from cord blood	blood
20	chr15:52944600-52965400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr15:52944600-52969800	Weak transcription	Fetal Brain Male	brain
22	chr15:52944800-52951000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:52944800-52952000	Strong transcription	Primary hematopoietic stem cells	blood
24	chr15:52945000-52965400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:52945000-52968600	Weak transcription	HepG2	liver
26	chr15:52945200-52950600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:52945200-52959800	Weak transcription	Dnd41	blood
28	chr15:52945400-52951200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:52945400-52951600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:52945400-52956600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:52945400-52965400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr15:52945600-52950800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:52945600-52956200	Weak transcription	Colonic Mucosa	Colon
34	chr15:52945600-52958400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:52945600-52962800	Strong transcription	Placenta	Placenta
36	chr15:52945800-52949600	Weak transcription	Fetal Intestine Large	intestine
37	chr15:52945800-52950800	Weak transcription	Fetal Muscle Leg	muscle
38	chr15:52945800-52951000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr15:52945800-52951000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:52945800-52951000	Weak transcription	Fetal Intestine Small	intestine
41	chr15:52945800-52951400	Strong transcription	Primary T cells from cord blood	blood
42	chr15:52945800-52951400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:52945800-52956800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:52946000-52949200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:52946000-52949400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:52946000-52949400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:52946000-52949600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:52946000-52950000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:52946000-52950000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:52946000-52950800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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