Variant report

Variant	rs1242499
Chromosome Location	chr17:17379267-17379268
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17377592..17379713-chr17:17402478..17404778,3	K562	blood:
2	chr17:17290560..17292342-chr17:17378041..17380234,2	MCF-7	breast:
3	chr17:17379236..17381999-chr17:17395224..17401626,6	MCF-7	breast:
4	chr17:17377768..17379317-chr17:17494319..17496372,2	K562	blood:
5	chr17:17360225..17362152-chr17:17377850..17379702,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133027	Chromatin interaction
ENSG00000264666	Chromatin interaction
ENSG00000108551	Chromatin interaction

Extended variants
information (count: 44 )
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];0.93[ASN][1000 genomes]
rs1242490	1.00[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];0.94[ASN][1000 genomes]
rs1242493	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1242498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1242500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1242501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1242502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];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];0.94[ASN][1000 genomes]
rs1242505	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1242506	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1242511	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1242514	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]
rs1242515	1.00[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];0.94[ASN][1000 genomes]
rs1242517	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1242518	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1263507	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.94[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];0.90[ASN][1000 genomes]
rs2232831	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2660836	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2694920	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2694926	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2694927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs28435349	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4479310	1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4646410	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs4924755	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4924868	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924877	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924890	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924891	1.00[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];0.92[ASN][1000 genomes]
rs711352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7219976	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7220132	1.00[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];0.91[ASN][1000 genomes]
rs7220217	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7946	0.81[TSI][hapmap]
rs8074074	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs8074191	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1242499	TNFRSF13B	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17363600-17380000	Weak transcription	Right Atrium	heart
2	chr17:17363800-17380200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:17372000-17380200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:17374400-17379400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:17374800-17380200	Weak transcription	Brain Substantia Nigra	brain
6	chr17:17376000-17379400	Weak transcription	Dnd41	blood
7	chr17:17376000-17380200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr17:17376000-17380200	Weak transcription	Fetal Brain Female	brain
9	chr17:17376000-17380200	Weak transcription	Gastric	stomach
10	chr17:17376000-17380400	Weak transcription	Fetal Brain Male	brain
11	chr17:17376200-17380000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr17:17376200-17380200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:17376200-17380200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr17:17376200-17380200	Weak transcription	Brain Angular Gyrus	brain
15	chr17:17376200-17380200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr17:17376400-17380200	Weak transcription	Brain Germinal Matrix	brain
17	chr17:17376600-17379400	Weak transcription	Brain Anterior Caudate	brain
18	chr17:17376600-17379400	Weak transcription	Hela-S3	cervix
19	chr17:17376600-17380200	Weak transcription	Brain Hippocampus Middle	brain
20	chr17:17378000-17380200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:17378000-17380200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr17:17378800-17379400	Weak transcription	Adipose Nuclei	Adipose
23	chr17:17378800-17380000	Enhancers	Spleen	Spleen
24	chr17:17379000-17379400	Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr17:17379000-17379800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr17:17379000-17380000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr17:17379200-17379600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr17:17379200-17379800	Enhancers	Brain Cingulate Gyrus	brain
29	chr17:17379200-17380000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:17379200-17380000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr17:17379200-17380200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr17:17379200-17380200	Weak transcription	Fetal Intestine Small	intestine

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