Variant report

Variant	rs16889173
Chromosome Location	chr6:36797956-36797957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12660067	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12664540	1.00[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13193613	0.84[GIH][hapmap]
rs16889183	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs16889199	0.84[GIH][hapmap]
rs35201827	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3822967	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6915283	1.00[YRI][hapmap]
rs6938178	0.81[MKK][hapmap];1.00[YRI][hapmap]
rs9470422	0.85[GIH][hapmap]

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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5261	chr6:36754545-36798824	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16889173	CLPS	cis	parietal	SCAN
rs16889173	OR10W1	trans	parietal	SCAN
rs16889173	CDKN1A	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36788400-36802400	Weak transcription	Fetal Kidney	kidney
2	chr6:36789800-36802200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:36790600-36799400	Enhancers	Fetal Muscle Leg	muscle
4	chr6:36791200-36805800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:36791400-36798000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:36795200-36798600	Enhancers	HUVEC	blood vessel
7	chr6:36795200-36802600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:36795400-36798800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:36795600-36798000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:36795800-36801800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr6:36795800-36802200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:36796000-36798000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:36796400-36802200	Weak transcription	Placenta	Placenta
14	chr6:36796600-36798000	Weak transcription	Gastric	stomach
15	chr6:36797000-36798000	Weak transcription	Right Ventricle	heart
16	chr6:36797000-36800000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr6:36797200-36798600	Enhancers	Fetal Intestine Small	intestine
18	chr6:36797400-36798600	Enhancers	Fetal Brain Male	brain
19	chr6:36797600-36798000	Enhancers	Adipose Nuclei	Adipose
20	chr6:36797600-36798000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr6:36797600-36798400	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr6:36797600-36798600	Enhancers	Liver	Liver
23	chr6:36797600-36798600	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr6:36797600-36798600	Enhancers	Fetal Intestine Large	intestine
25	chr6:36797600-36798600	Enhancers	Fetal Lung	lung
26	chr6:36797600-36798600	Enhancers	Stomach Mucosa	stomach
27	chr6:36797600-36798800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:36797600-36798800	Enhancers	Brain Hippocampus Middle	brain
29	chr6:36797600-36798800	Enhancers	Fetal Brain Female	brain
30	chr6:36797600-36798800	Enhancers	Fetal Stomach	stomach
31	chr6:36797600-36798800	Enhancers	Right Atrium	heart
32	chr6:36797600-36798800	Flanking Active TSS	HepG2	liver
33	chr6:36797800-36798000	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr6:36797800-36798000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr6:36797800-36798000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:36797800-36798000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:36797800-36798000	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr6:36797800-36798000	Enhancers	Brain Cingulate Gyrus	brain
39	chr6:36797800-36798000	Enhancers	HSMM	muscle
40	chr6:36797800-36798000	Enhancers	Osteobl	bone
41	chr6:36797800-36798200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr6:36797800-36798200	Enhancers	Brain Substantia Nigra	brain
43	chr6:36797800-36798200	Flanking Active TSS	Fetal Heart	heart
44	chr6:36797800-36798200	Flanking Active TSS	Fetal Muscle Trunk	muscle
45	chr6:36797800-36798200	Enhancers	Fetal Thymus	thymus
46	chr6:36797800-36798200	Enhancers	Spleen	Spleen
47	chr6:36797800-36798400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr6:36797800-36798400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:36797800-36798400	Enhancers	Muscle Satellite Cultured Cells	--
50	chr6:36797800-36798400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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