Variant report

Variant	rs9923616
Chromosome Location	chr16:74538589-74538590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:74536407..74538913-chr16:74540581..74542783,4	K562	blood:
2	chr16:74536407..74538913-chr16:74541075..74542783,2	K562	blood:
3	chr16:74535608..74538599-chr16:74639550..74642585,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090863	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1019572	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1019573	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs10500587	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11149722	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11639812	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11640021	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11641958	0.95[ASN][1000 genomes]
rs11643293	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11644298	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11648786	0.83[ASN][1000 genomes]
rs11648868	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12325017	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12445991	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs12446054	1.00[JPT][hapmap]
rs12446095	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12447531	0.85[ASN][1000 genomes]
rs12448026	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs12449071	0.95[ASN][1000 genomes]
rs12449125	0.86[ASN][1000 genomes]
rs12598701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12716768	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12927939	0.94[ASN][1000 genomes]
rs12930645	0.92[ASN][1000 genomes]
rs13339161	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13339456	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13359	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13380609	0.93[ASN][1000 genomes]
rs1469140	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17672539	0.94[ASN][1000 genomes]
rs1971071	0.82[AMR][1000 genomes]
rs1985611	0.86[ASN][1000 genomes]
rs2098754	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2288053	1.00[JPT][hapmap]
rs2303275	1.00[JPT][hapmap]
rs2303278	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2303281	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2549063	0.84[AMR][1000 genomes]
rs2549559	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2550816	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28762730	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3096409	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3785312	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3826239	0.87[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3851729	0.92[JPT][hapmap]
rs3960602	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3973385	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4072222	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4072450	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4243108	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs4438331	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs4600490	1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap]
rs4887772	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887776	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4887777	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4887779	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4888238	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs4888240	0.92[JPT][hapmap]
rs4888242	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs4888253	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4888256	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs4888262	0.92[JPT][hapmap]
rs4888265	0.85[JPT][hapmap]
rs4888266	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4888267	0.83[JPT][hapmap]
rs4888274	0.86[JPT][hapmap]
rs6564117	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs6564154	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs6564157	0.84[CHB][hapmap]
rs7185026	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7188050	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7188197	0.88[ASN][1000 genomes]
rs7189123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7190577	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7191665	0.92[JPT][hapmap]
rs7193959	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7194143	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7195020	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7195196	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7195198	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7201320	0.86[JPT][hapmap]
rs7203452	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs7204382	0.90[CHB][hapmap]
rs7204804	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs7205258	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs7342732	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs7978	0.86[JPT][hapmap]
rs8045653	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8045848	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs8050624	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs8052923	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs8053599	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8055784	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs8058133	0.86[JPT][hapmap]
rs8058692	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs8058922	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs8059869	0.92[JPT][hapmap]
rs8062783	0.86[JPT][hapmap]
rs918782	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9888976	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs9923145	0.92[JPT][hapmap]
rs9927073	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs9929483	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs9931225	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9932831	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs9938833	0.91[CHB][hapmap];0.92[JPT][hapmap]

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	nsv948443	chr16:73994997-74627711	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1065964	chr16:74088091-74575604	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
4	esv2758431	chr16:74334780-74587185	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2758656	chr16:74334780-74587185	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv428806	chr16:74394226-74580125	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv833278	chr16:74415944-74584123	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv1060629	chr16:74483574-74660669	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv1062517	chr16:74483574-74710623	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv833279	chr16:74490746-74663073	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS 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	20 gene(s)	inside rSNPs	diseases
12	nsv978169	chr16:74507776-74560104	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	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
14	nsv906905	chr16:74527618-74679244	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9923616	RFWD3	cis	Esophagus Mucosa	GTEx
rs9923616	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs9923616	RFWD3	cis	Skin Sun Exposed Lower leg	GTEx
rs9923616	RFWD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74485600-74542600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:74498800-74544400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:74499200-74539200	Strong transcription	Primary B cells from peripheral blood	blood
4	chr16:74508600-74544000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr16:74522000-74542400	Weak transcription	NHDF-Ad	bronchial
6	chr16:74522000-74544600	Weak transcription	Right Ventricle	heart
7	chr16:74525200-74539600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr16:74525200-74542000	Weak transcription	K562	blood
9	chr16:74525200-74565200	Weak transcription	Fetal Brain Male	brain
10	chr16:74525400-74543000	Weak transcription	NHLF	lung
11	chr16:74525400-74561000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr16:74525400-74572200	Weak transcription	HUVEC	blood vessel
13	chr16:74526400-74544000	Weak transcription	Fetal Brain Female	brain
14	chr16:74527200-74541400	Weak transcription	Esophagus	oesophagus
15	chr16:74527200-74544600	Weak transcription	Gastric	stomach
16	chr16:74527200-74544800	Weak transcription	Ovary	ovary
17	chr16:74527200-74545800	Weak transcription	Spleen	Spleen
18	chr16:74527200-74555600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr16:74527400-74539200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr16:74527400-74554600	Weak transcription	HSMMtube	muscle
21	chr16:74528000-74547600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr16:74528200-74539400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr16:74528200-74541800	Weak transcription	Left Ventricle	heart
24	chr16:74528400-74555800	Weak transcription	Small Intestine	intestine
25	chr16:74530000-74544800	Weak transcription	A549	lung
26	chr16:74530400-74546200	Weak transcription	Lung	lung
27	chr16:74530600-74544000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr16:74530800-74542000	Weak transcription	HSMM	muscle
29	chr16:74530800-74558600	Weak transcription	Fetal Lung	lung
30	chr16:74532800-74539200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr16:74533000-74539400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr16:74533000-74539600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr16:74533200-74543000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr16:74533600-74539400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr16:74534000-74539800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr16:74534600-74539200	Strong transcription	Primary T cells from cord blood	blood
37	chr16:74534600-74539200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr16:74534800-74539200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr16:74534800-74539200	Strong transcription	Fetal Thymus	thymus
40	chr16:74535000-74538800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr16:74535000-74539000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr16:74535000-74539200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr16:74535000-74539200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr16:74535000-74539200	Strong transcription	GM12878-XiMat	blood
45	chr16:74535200-74538800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr16:74535200-74539200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr16:74535200-74539200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr16:74535200-74539600	Strong transcription	Fetal Intestine Large	intestine
49	chr16:74535400-74538800	Strong transcription	Fetal Muscle Leg	muscle
50	chr16:74535400-74539400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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