Variant report

Variant	rs1242514
Chromosome Location	chr17:17384500-17384501
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17379018..17381864-chr17:17382301..17386049,5	MCF-7	breast:
2	chr17:17384082..17386692-chr17:17387080..17388772,2	MCF-7	breast:
3	chr17:17349350..17351226-chr17:17382738..17384846,2	K562	blood:
4	chr17:17382327..17386627-chr17:17397610..17400464,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141026	Chromatin interaction
ENSG00000108551	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11652200	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1242490	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242493	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1242498	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1242499	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1242500	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1242501	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1242502	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1242503	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1242505	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1242506	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1242511	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1242515	0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242517	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1242518	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1263507	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1263509	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12938634	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232831	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2660836	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2694920	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2694926	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2694927	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28435349	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4479310	0.90[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4646410	0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs4924755	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924868	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924877	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924890	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924891	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs711352	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7219976	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7220132	0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7220217	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7946	0.81[TSI][hapmap]
rs8074074	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs8074191	0.80[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065710	chr17:17328111-17391443	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv907729	chr17:17338536-17425279	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv907730	chr17:17358004-17415217	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv827909	chr17:17358945-17394331	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv907732	chr17:17381764-17415217	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv907733	chr17:17381764-17422608	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv907734	chr17:17381764-17425858	Enhancers Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv907735	chr17:17381764-17448589	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv907736	chr17:17381764-17465458	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1242514	TNFRSF13B	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17380400-17385600	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr17:17381200-17386600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr17:17381200-17391000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:17381200-17394200	Weak transcription	Ovary	ovary
5	chr17:17381200-17394400	Weak transcription	Aorta	Aorta
6	chr17:17381200-17395400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr17:17381200-17397000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:17381400-17385800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr17:17381400-17386600	Enhancers	Thymus	Thymus
10	chr17:17381400-17388800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr17:17381400-17389400	Genic enhancers	Fetal Thymus	thymus
12	chr17:17381400-17392200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr17:17381400-17394400	Weak transcription	Colonic Mucosa	Colon
14	chr17:17381400-17397000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr17:17381600-17384600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:17381600-17385000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr17:17381600-17386200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr17:17381600-17387400	Weak transcription	HSMMtube	muscle
19	chr17:17381600-17387600	Weak transcription	Esophagus	oesophagus
20	chr17:17381600-17388800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:17381600-17394800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr17:17381800-17384600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr17:17381800-17384600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr17:17381800-17384600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr17:17381800-17384600	Enhancers	HMEC	breast
26	chr17:17381800-17384800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr17:17381800-17385600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:17381800-17387400	Weak transcription	HSMM	muscle
29	chr17:17381800-17387800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr17:17381800-17388000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr17:17381800-17388000	Enhancers	Fetal Heart	heart
32	chr17:17381800-17388600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr17:17381800-17389800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr17:17381800-17391000	Weak transcription	Fetal Kidney	kidney
35	chr17:17381800-17391000	Weak transcription	NHDF-Ad	bronchial
36	chr17:17381800-17393800	Weak transcription	Fetal Lung	lung
37	chr17:17381800-17396200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr17:17381800-17397200	Weak transcription	NH-A	brain
39	chr17:17382000-17385000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr17:17382000-17387800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr17:17382000-17390800	Weak transcription	Brain Substantia Nigra	brain
42	chr17:17382000-17391000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr17:17382000-17391000	Weak transcription	Placenta	Placenta
44	chr17:17382000-17391000	Weak transcription	Osteobl	bone
45	chr17:17382400-17385800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr17:17382400-17387600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr17:17382400-17388200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr17:17382400-17388800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr17:17382400-17396400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr17:17382600-17384600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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