Variant report

Variant	rs997972
Chromosome Location	chr20:16561203-16561204
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	chr20:16550509..16554024-chr20:16560848..16563415,3	MCF-7	breast:
2	chr20:16554484..16557263-chr20:16559352..16563570,6	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1007144	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs13042615	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs13044683	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179905	0.97[EUR][1000 genomes]
rs2328045	0.99[EUR][1000 genomes]
rs34548254	0.99[EUR][1000 genomes]
rs34678561	0.97[EUR][1000 genomes]
rs35610860	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4813225	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55776240	0.99[EUR][1000 genomes]
rs6034535	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6034539	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6044121	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6044124	1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6044128	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6044141	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6044146	0.96[EUR][1000 genomes]
rs6105631	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6111190	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6111195	0.97[EUR][1000 genomes]
rs6514692	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6514693	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs926772	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926773	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762064	chr20:16558260-16568062	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
2	nsv1058496	chr20:16558260-16575531	Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv517032	chr20:16560990-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	nsv585650	chr20:16561203-16585314	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs997972	KIF16B	cis	cerebellum	SCAN
rs997972	KIF16B	cis	multi-tissue	Pritchard
rs997972	LOC100130264	cis	cerebellum	SCAN
rs997972	KIF16B	cis	Whole Blood	GTEx
rs997972	C20orf23	Cis_1M	lymphoblastoid	RTeQTL
rs997972	KIF16B	cis	Muscle Skeletal	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16556400-16562400	Weak transcription	Left Ventricle	heart
2	chr20:16559400-16562000	Enhancers	Fetal Intestine Large	intestine
3	chr20:16559600-16561800	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr20:16559600-16561800	Enhancers	NHDF-Ad	bronchial
5	chr20:16559600-16562000	Enhancers	Duodenum Mucosa	Duodenum
6	chr20:16559600-16562000	Enhancers	Fetal Intestine Small	intestine
7	chr20:16559600-16562200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr20:16559800-16562000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr20:16559800-16562200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr20:16559800-16564600	Enhancers	Fetal Brain Male	brain
11	chr20:16559800-16567000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr20:16560000-16561400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:16560000-16561600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr20:16560000-16561600	Enhancers	HMEC	breast
15	chr20:16560000-16561800	Enhancers	Osteobl	bone
16	chr20:16560000-16562000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr20:16560000-16562000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr20:16560000-16562000	Enhancers	Stomach Mucosa	stomach
19	chr20:16560000-16562200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr20:16560000-16562200	Enhancers	NHEK	skin
21	chr20:16560000-16562400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr20:16560000-16562600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr20:16560200-16561400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr20:16560200-16561400	Enhancers	HSMMtube	muscle
25	chr20:16560200-16561600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr20:16560200-16561600	Enhancers	Brain Germinal Matrix	brain
27	chr20:16560200-16561600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr20:16560200-16561600	Enhancers	NHLF	lung
29	chr20:16560200-16562200	Enhancers	Fetal Lung	lung
30	chr20:16560400-16561600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr20:16560400-16561600	Enhancers	Hela-S3	cervix
32	chr20:16560600-16561400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr20:16560600-16561400	Enhancers	A549	lung
34	chr20:16560600-16561600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr20:16560800-16561600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr20:16560800-16561600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr20:16560800-16561600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr20:16560800-16561600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr20:16560800-16561600	Enhancers	Adipose Nuclei	Adipose
40	chr20:16560800-16561600	Enhancers	Fetal Brain Female	brain
41	chr20:16560800-16561600	Enhancers	Fetal Stomach	stomach
42	chr20:16560800-16561600	Enhancers	Lung	lung
43	chr20:16560800-16561600	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr20:16560800-16561800	Weak transcription	NH-A	brain
45	chr20:16560800-16562000	Enhancers	Colon Smooth Muscle	Colon
46	chr20:16560800-16562200	Enhancers	Stomach Smooth Muscle	stomach
47	chr20:16561000-16561400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr20:16561000-16562400	Enhancers	Fetal Muscle Leg	muscle
49	chr20:16561200-16561600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr20:16561200-16561800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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