Variant report

Variant	rs9923034
Chromosome Location	chr16:75403341-75403342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:75402989..75403657-chr4:99558827..99559504,2	MCF-7	breast:
2	chr16:75400892..75404468-chr16:75404804..75409122,4	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10438605	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11149817	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12149472	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149940	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12444789	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445803	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12716785	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12918234	0.86[ASN][1000 genomes]
rs12919055	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12921808	1.00[ASN][1000 genomes]
rs12926447	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12928461	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12935491	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13337069	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13339257	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17605695	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17674216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285221	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2550325	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2550916	1.00[ASN][1000 genomes]
rs2650408	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2650409	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28368934	0.90[ASN][1000 genomes]
rs28371085	0.85[EUR][1000 genomes]
rs28510780	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28525459	0.93[ASN][1000 genomes]
rs34532060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35255668	0.87[EUR][1000 genomes]
rs4081763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383172	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55715607	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55719515	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59800961	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60544814	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6625	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71380715	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7184596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7185880	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7186825	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7188111	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7189037	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7206589	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206780	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs729109	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8046261	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047147	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8047983	0.93[ASN][1000 genomes]
rs8048683	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050367	0.89[ASN][1000 genomes]
rs8051151	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052405	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052555	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054557	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8055098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8056345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056473	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8057652	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8057925	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8059427	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8059883	0.93[ASN][1000 genomes]
rs8060338	0.93[ASN][1000 genomes]
rs8063733	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9319483	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9319484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9745455	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921115	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9923574	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924524	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926453	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9926933	0.93[ASN][1000 genomes]
rs9927330	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928744	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928901	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930002	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9932982	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9935954	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9935967	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936641	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936648	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936853	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9937903	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9938936	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939080	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939587	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9940189	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940884	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941142	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	esv2762265	chr16:75368897-75415866	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
7	esv2422358	chr16:75381762-75456763	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
9	nsv525232	chr16:75402361-75439132	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv525466	chr16:75402361-75439132	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9923034	RP11-252K23.2	cis	Nerve Tibial	GTEx
rs9923034	RP11-252K23.2	cis	Thyroid	GTEx
rs9923034	RP11-252K23.2	cis	Esophagus Mucosa	GTEx
rs9923034	RP11-252K23.2	cis	Artery Tibial	GTEx
rs9923034	RP11-252K23.2	cis	Adipose Subcutaneous	GTEx
rs9923034	RP11-252K23.2	cis	lung	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75338800-75426400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr16:75339400-75411800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr16:75354800-75413600	Weak transcription	Fetal Thymus	thymus
4	chr16:75358400-75421400	Weak transcription	K562	blood
5	chr16:75368600-75411400	Weak transcription	GM12878-XiMat	blood
6	chr16:75368600-75412800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr16:75368800-75409800	Weak transcription	Thymus	Thymus
8	chr16:75368800-75413200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr16:75369200-75406000	Weak transcription	Dnd41	blood
10	chr16:75375800-75408400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr16:75376600-75410600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr16:75376600-75426800	Weak transcription	Brain Germinal Matrix	brain
13	chr16:75377000-75411600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr16:75377000-75411800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr16:75377000-75424400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr16:75377000-75426400	Weak transcription	Gastric	stomach
17	chr16:75377200-75424000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr16:75377400-75426400	Weak transcription	Pancreas	Pancrea
19	chr16:75377600-75405000	Weak transcription	Liver	Liver
20	chr16:75377600-75407600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr16:75377600-75410200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr16:75377600-75411800	Weak transcription	Left Ventricle	heart
23	chr16:75377800-75405000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr16:75378000-75410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr16:75378000-75411000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr16:75378400-75410400	Weak transcription	Fetal Kidney	kidney
27	chr16:75378600-75409600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr16:75380200-75411400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr16:75380200-75413200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr16:75381200-75403400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr16:75381400-75409400	Weak transcription	Placenta	Placenta
32	chr16:75385600-75404800	Weak transcription	Hela-S3	cervix
33	chr16:75385600-75405800	Weak transcription	NHDF-Ad	bronchial
34	chr16:75385800-75404800	Weak transcription	Osteobl	bone
35	chr16:75385800-75405000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr16:75385800-75405800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr16:75385800-75406200	Weak transcription	HSMM	muscle
38	chr16:75385800-75409600	Weak transcription	NHEK	skin
39	chr16:75387000-75406600	Weak transcription	A549	lung
40	chr16:75388400-75409800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr16:75390600-75410800	Weak transcription	Small Intestine	intestine
42	chr16:75391600-75406200	Weak transcription	Colon Smooth Muscle	Colon
43	chr16:75391800-75411800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr16:75392200-75411400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr16:75392400-75422000	Weak transcription	Aorta	Aorta
46	chr16:75392800-75405000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr16:75393600-75410800	Weak transcription	Brain Hippocampus Middle	brain
48	chr16:75393800-75406200	Weak transcription	Psoas Muscle	Psoas
49	chr16:75394600-75406200	Weak transcription	HUVEC	blood vessel
50	chr16:75395600-75412400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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