Variant report

Variant	rs17016207
Chromosome Location	chr4:143405082-143405083
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143403314..143405923-chr4:143409860..143412488,3	MCF-7	breast:
2	chr4:143402650..143405583-chr4:143767540..143769088,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10012476	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10015184	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1013397	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12642500	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12643136	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12644565	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12646243	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12649139	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1364917	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1364918	1.00[CEU][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1364919	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1364920	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1364926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1425534	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1425535	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1425538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17016170	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17016248	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17016284	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17016304	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17016306	0.82[JPT][hapmap]
rs2042644	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2113997	0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2162108	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2322705	0.89[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2322706	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2322796	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28510314	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28823374	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28850298	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28861843	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34900920	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3913164	0.87[CEU][hapmap]
rs4345256	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57724540	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59784151	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60004938	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6823362	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7668133	0.89[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7672965	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7695918	0.86[CEU][hapmap]
rs7699408	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9308152	0.81[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs931637	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs979511	0.87[CEU][hapmap];0.81[CHD][hapmap]
rs9986090	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9998089	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17016207	CAMSAP1	trans	parietal	SCAN
rs17016207	INPP4B	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143369200-143410600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:143396800-143406000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr4:143396800-143406800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:143397000-143406200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:143397200-143406000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr4:143397400-143414800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:143401800-143418600	Weak transcription	Fetal Heart	heart
8	chr4:143402800-143406400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:143403600-143406200	Weak transcription	Fetal Intestine Small	intestine
10	chr4:143403600-143406400	Weak transcription	Fetal Intestine Large	intestine
11	chr4:143404000-143406200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:143404600-143406800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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