Variant report

Variant	rs2303223
Chromosome Location	chr16:31075175-31075176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31072499..31076258-chr16:31082404..31085688,4	K562	blood:
2	chr16:31053220..31057176-chr16:31073803..31076480,4	MCF-7	breast:
3	chr16:31073473..31075670-chr16:31469255..31471043,2	MCF-7	breast:
4	chr16:31043007..31053782-chr16:31072765..31087431,40	MCF-7	breast:
5	chr16:31062123..31065063-chr16:31072839..31075736,2	MCF-7	breast:
6	chr16:31073574..31075924-chr16:31127907..31130567,2	K562	blood:

Variant related genes	Relation type
ENSG00000103510	Chromatin interaction
ENSG00000167394	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000262766	Chromatin interaction
ENSG00000260911	Chromatin interaction
ENSG00000103496	Chromatin interaction

Extended variants
information (count: 146 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1046276	1.00[JPT][hapmap]
rs1060506	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10782001	0.89[JPT][hapmap]
rs10782002	0.89[JPT][hapmap]
rs10871454	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11076	0.88[JPT][hapmap]
rs1108431	0.86[ASN][1000 genomes]
rs11150599	0.88[JPT][hapmap]
rs11150600	0.89[JPT][hapmap]
rs11150601	0.89[JPT][hapmap]
rs11150604	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11640534	0.89[JPT][hapmap]
rs11640767	0.88[ASN][1000 genomes]
rs11640957	0.88[ASN][1000 genomes]
rs11640961	0.86[CEU][hapmap];0.89[JPT][hapmap]
rs11642003	0.84[ASN][1000 genomes]
rs11642192	0.95[ASN][1000 genomes]
rs11647284	0.98[ASN][1000 genomes]
rs11647442	0.93[ASN][1000 genomes]
rs11649653	1.00[JPT][hapmap]
rs11862744	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11864806	0.98[ASN][1000 genomes]
rs11864839	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11865038	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11865499	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12445650	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12448321	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12597511	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12716981	0.93[ASN][1000 genomes]
rs12716982	0.93[ASN][1000 genomes]
rs12924903	1.00[JPT][hapmap]
rs12926295	0.88[JPT][hapmap]
rs12928852	0.89[JPT][hapmap]
rs12931046	0.89[JPT][hapmap]
rs12934418	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13708	0.89[JPT][hapmap]
rs14235	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1458201	0.89[JPT][hapmap]
rs1458202	0.89[JPT][hapmap]
rs1549293	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17839567	0.86[ASN][1000 genomes]
rs17839568	0.98[ASN][1000 genomes]
rs1870293	0.89[JPT][hapmap]
rs1978485	0.93[ASN][1000 genomes]
rs1978487	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2032915	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2054213	0.89[JPT][hapmap]
rs2288004	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303222	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305880	0.89[JPT][hapmap]
rs2305884	0.89[JPT][hapmap]
rs2359612	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2855475	0.87[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28725459	0.89[ASN][1000 genomes]
rs28814987	0.98[ASN][1000 genomes]
rs2884738	0.93[ASN][1000 genomes]
rs34649473	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34898535	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35351013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35468353	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs35675346	1.00[JPT][hapmap]
rs35713203	0.98[ASN][1000 genomes]
rs3751855	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4468641	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4527034	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4889525	0.89[JPT][hapmap]
rs4889530	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4889599	0.89[JPT][hapmap]
rs4889603	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs4889604	0.89[JPT][hapmap]
rs4889606	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs4889609	1.00[JPT][hapmap]
rs4889619	0.82[ASN][1000 genomes]
rs4889620	0.93[ASN][1000 genomes]
rs4889651	0.88[JPT][hapmap]
rs4889653	0.88[JPT][hapmap]
rs55766044	0.93[ASN][1000 genomes]
rs55979739	0.86[ASN][1000 genomes]
rs56284083	0.86[ASN][1000 genomes]
rs56314408	0.93[ASN][1000 genomes]
rs56813533	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57434408	0.93[ASN][1000 genomes]
rs58726213	0.84[ASN][1000 genomes]
rs59061704	0.88[ASN][1000 genomes]
rs59735493	0.93[ASN][1000 genomes]
rs60996860	0.89[ASN][1000 genomes]
rs61162043	0.98[ASN][1000 genomes]
rs61320757	0.93[ASN][1000 genomes]
rs6565217	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6950	0.89[JPT][hapmap]
rs7187995	0.91[ASN][1000 genomes]
rs7196161	0.98[ASN][1000 genomes]
rs7196726	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7197717	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7199949	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7200879	1.00[JPT][hapmap]
rs7203999	0.89[JPT][hapmap]
rs7204459	0.89[JPT][hapmap]
rs7206511	0.89[JPT][hapmap]
rs7294	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs729482	1.00[JPT][hapmap]
rs732172	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs732173	0.86[ASN][1000 genomes]
rs73530203	0.95[ASN][1000 genomes]
rs749670	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs749671	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs749767	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7500176	0.86[ASN][1000 genomes]
rs750952	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8046707	0.89[JPT][hapmap]
rs8047803	0.98[ASN][1000 genomes]
rs8050588	0.89[JPT][hapmap]
rs8050894	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8056842	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8060857	0.89[JPT][hapmap]
rs8061047	0.95[ASN][1000 genomes]
rs8062719	0.89[JPT][hapmap]
rs8063565	0.88[JPT][hapmap]
rs881929	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs889548	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs889555	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs897986	0.89[JPT][hapmap]
rs9923231	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9925964	0.95[CEU][hapmap];0.93[ASN][1000 genomes]
rs9926533	0.96[CEU][hapmap];0.89[JPT][hapmap]
rs9929899	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9933843	0.88[JPT][hapmap]
rs9934438	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9936329	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9939417	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9939558	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9972727	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
4	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
5	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
6	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
7	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
8	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
9	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
10	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
11	nsv833193	chr16:30960796-31133604	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
12	nsv916994	chr16:30971725-31078117	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
13	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
14	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh 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	202 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2303223	RP11-196G11.2	cis	Muscle Skeletal	GTEx
rs2303223	KAT8	cis	Skin Sun Exposed Lower leg	GTEx
rs2303223	HSD3B7	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31046000-31083200	Weak transcription	Right Atrium	heart
2	chr16:31049600-31075600	Weak transcription	Psoas Muscle	Psoas
3	chr16:31051400-31083000	Weak transcription	Fetal Lung	lung
4	chr16:31052000-31083400	Weak transcription	Primary B cells from cord blood	blood
5	chr16:31054000-31083200	Weak transcription	Fetal Kidney	kidney
6	chr16:31054200-31076200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr16:31063800-31076200	Weak transcription	K562	blood
8	chr16:31064400-31075400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr16:31064400-31075400	Weak transcription	HUVEC	blood vessel
10	chr16:31068800-31075200	Strong transcription	Fetal Stomach	stomach
11	chr16:31069000-31076200	Strong transcription	Fetal Intestine Small	intestine
12	chr16:31069200-31075600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr16:31069600-31075200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr16:31070400-31082600	Weak transcription	Fetal Brain Male	brain
15	chr16:31071000-31075400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr16:31071000-31075400	Strong transcription	Osteobl	bone
17	chr16:31071000-31075600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr16:31071000-31075800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr16:31071000-31075800	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr16:31071000-31076400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:31071000-31076800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr16:31071200-31075600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr16:31071200-31075600	Strong transcription	Brain Angular Gyrus	brain
24	chr16:31071200-31076600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr16:31071400-31075600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr16:31071400-31076000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr16:31071400-31076000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr16:31071600-31075400	Strong transcription	NHEK	skin
29	chr16:31071600-31075800	Strong transcription	Fetal Brain Female	brain
30	chr16:31071600-31076000	Strong transcription	Dnd41	blood
31	chr16:31071800-31075200	Strong transcription	Thymus	Thymus
32	chr16:31071800-31075400	Strong transcription	GM12878-XiMat	blood
33	chr16:31071800-31075600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr16:31071800-31075800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr16:31071800-31076600	Strong transcription	Brain Germinal Matrix	brain
36	chr16:31072000-31075200	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr16:31072000-31075600	Strong transcription	Brain Anterior Caudate	brain
38	chr16:31072000-31075600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr16:31072000-31076200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr16:31072000-31076600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr16:31072200-31075600	Strong transcription	Liver	Liver
42	chr16:31072200-31075800	Strong transcription	Pancreas	Pancrea
43	chr16:31072200-31075800	Weak transcription	Hela-S3	cervix
44	chr16:31072200-31076200	Genic enhancers	Fetal Muscle Leg	muscle
45	chr16:31072800-31075200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr16:31072800-31075400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr16:31072800-31076400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr16:31073000-31075200	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr16:31073200-31076800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr16:31073400-31075200	Weak transcription	Rectal Mucosa Donor 29	rectum

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