Variant report

Variant	rs204606
Chromosome Location	chr20:14317679-14317680
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1040826	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs17263597	0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs1998238	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs2038505	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs204605	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs204617	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs204625	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs204632	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs204633	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs204638	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs204639	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs204643	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2208453	0.90[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2208455	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2256118	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2327841	0.82[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs2327842	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2327843	0.81[AMR][1000 genomes]
rs2327845	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2423779	0.90[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2876376	0.81[ASN][1000 genomes]
rs370158	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs382674	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4384860	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4814293	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs485293	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs6033926	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs6033927	0.82[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap]
rs6033931	0.82[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes]
rs6033932	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6033933	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6033941	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042629	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs6042630	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6042642	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs6042648	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6042652	0.84[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6042653	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6042669	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6074719	0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6074720	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6074721	0.89[ASN][1000 genomes]
rs6074722	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6079355	0.81[CHB][hapmap]
rs6079380	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6135113	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs615331	0.82[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs717327	0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs718705	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7263144	0.82[CEU][hapmap]
rs8123052	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs982553	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs982554	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs994567	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1057486	chr20:14077828-14469129	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1066235	chr20:14173771-14389050	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv432101	chr20:14294196-14353346	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv1799128	chr20:14309952-14324140	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs204606	KIF16B	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14303600-14323400	Weak transcription	Small Intestine	intestine
2	chr20:14311800-14318600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr20:14312200-14318400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr20:14312800-14318400	Active TSS	HMEC	breast
5	chr20:14313200-14318400	Active TSS	Fetal Intestine Large	intestine
6	chr20:14313400-14318400	Active TSS	Fetal Intestine Small	intestine
7	chr20:14313400-14318600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:14313600-14318400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:14313600-14318400	Active TSS	Brain Anterior Caudate	brain
10	chr20:14313600-14318400	Active TSS	Brain Hippocampus Middle	brain
11	chr20:14313600-14318400	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr20:14313600-14318400	Active TSS	Colon Smooth Muscle	Colon
13	chr20:14313600-14318400	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr20:14313600-14318400	Active TSS	Fetal Stomach	stomach
15	chr20:14313600-14318600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr20:14313600-14318600	Active TSS	Brain Angular Gyrus	brain
17	chr20:14313600-14318600	Active TSS	Stomach Smooth Muscle	stomach
18	chr20:14313800-14318400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr20:14313800-14318400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr20:14313800-14318600	Active TSS	Fetal Kidney	kidney
21	chr20:14313800-14318800	Active TSS	Ovary	ovary
22	chr20:14314000-14317800	Active TSS	Rectal Smooth Muscle	rectum
23	chr20:14314000-14318400	Active TSS	NHLF	lung
24	chr20:14314200-14318400	Active TSS	Fetal Muscle Leg	muscle
25	chr20:14314400-14318400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr20:14314400-14318400	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr20:14314400-14318400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr20:14314400-14318400	Active TSS	Duodenum Mucosa	Duodenum
29	chr20:14314400-14318400	Active TSS	Fetal Heart	heart
30	chr20:14314400-14318600	Active TSS	Brain Cingulate Gyrus	brain
31	chr20:14314600-14318400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr20:14314800-14318400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr20:14314800-14318600	Active TSS	A549	lung
34	chr20:14315000-14318400	Active TSS	NHEK	skin
35	chr20:14315200-14318400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr20:14315600-14318600	Active TSS	NHDF-Ad	bronchial
37	chr20:14315800-14318400	Active TSS	Fetal Brain Male	brain
38	chr20:14315800-14318400	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr20:14316000-14318000	Active TSS	H1 Cell Line	embryonic stem cell
40	chr20:14316000-14318400	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr20:14316000-14318400	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr20:14316000-14318400	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr20:14316400-14318400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr20:14316600-14318600	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr20:14317000-14317800	Flanking Active TSS	Fetal Brain Female	brain
46	chr20:14317000-14318400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr20:14317000-14318400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr20:14317000-14318400	Active TSS	Fetal Thymus	thymus
49	chr20:14317000-14318400	Active TSS	Placenta Amnion	Placenta Amnion
50	chr20:14317000-14318400	Active TSS	Rectal Mucosa Donor 29	rectum

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