Variant report

Variant	rs17671618
Chromosome Location	chr20:16405098-16405099
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10485553	0.90[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10485555	1.00[JPT][hapmap]
rs12480660	1.00[JPT][hapmap]
rs12480678	1.00[JPT][hapmap]
rs12624346	0.90[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12624938	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs1555195	1.00[JPT][hapmap]
rs16997595	0.86[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs17671977	0.90[CEU][hapmap];0.97[EUR][1000 genomes]
rs17672161	0.90[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17737952	1.00[CHD][hapmap]
rs17740473	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1998085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2144896	1.00[JPT][hapmap]
rs2180472	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34122290	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34550969	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4814484	0.82[TSI][hapmap]
rs56329134	0.97[EUR][1000 genomes]
rs6034476	0.90[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs6034498	1.00[JPT][hapmap]
rs6044009	1.00[JPT][hapmap]
rs6044021	1.00[JPT][hapmap]
rs6080290	1.00[JPT][hapmap]
rs6080299	1.00[JPT][hapmap]
rs6111025	1.00[CHB][hapmap]
rs6111116	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs61664184	0.99[EUR][1000 genomes]
rs7262082	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs7268027	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs73898731	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73898736	0.97[EUR][1000 genomes]
rs73898746	0.96[EUR][1000 genomes]
rs8118656	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8120353	0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs8121801	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs8125188	0.98[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833931	chr20:16308276-16460596	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17671618	LOC149620	trans	parietal	SCAN
rs17671618	C20orf12	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16384000-16432600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr20:16387000-16406400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr20:16387400-16411800	Weak transcription	Colonic Mucosa	Colon
4	chr20:16391600-16406400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:16391600-16410800	Weak transcription	Thymus	Thymus
6	chr20:16391800-16409800	Weak transcription	Brain Angular Gyrus	brain
7	chr20:16391800-16414600	Weak transcription	Colon Smooth Muscle	Colon
8	chr20:16392000-16405600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr20:16392000-16406400	Weak transcription	Brain Anterior Caudate	brain
10	chr20:16392000-16407000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr20:16392200-16412800	Weak transcription	Fetal Kidney	kidney
12	chr20:16392200-16453000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr20:16392400-16411600	Weak transcription	Brain Substantia Nigra	brain
14	chr20:16393800-16408200	Weak transcription	Small Intestine	intestine
15	chr20:16395200-16411400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr20:16396000-16411400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr20:16396200-16412800	Weak transcription	NHDF-Ad	bronchial
18	chr20:16396400-16411000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr20:16396600-16406800	Weak transcription	Placenta	Placenta
20	chr20:16397400-16412000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr20:16398200-16417000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr20:16398200-16431000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr20:16399800-16405400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr20:16400000-16440000	Weak transcription	NHEK	skin
25	chr20:16400200-16414000	Weak transcription	Fetal Brain Female	brain
26	chr20:16401000-16414200	Weak transcription	Fetal Brain Male	brain
27	chr20:16401200-16408200	Weak transcription	HSMMtube	muscle
28	chr20:16401200-16417000	Weak transcription	Brain Germinal Matrix	brain
29	chr20:16402400-16408200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr20:16402600-16410200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr20:16402600-16412200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr20:16402800-16412800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr20:16402800-16412800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr20:16402800-16413600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr20:16403000-16413000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr20:16403200-16406400	Weak transcription	Psoas Muscle	Psoas
37	chr20:16403200-16408200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr20:16403200-16408600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr20:16403200-16409200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr20:16403200-16409200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr20:16403600-16410600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr20:16404000-16406400	Strong transcription	Liver	Liver
43	chr20:16404000-16406600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr20:16404000-16410200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr20:16404000-16410200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr20:16404000-16410800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr20:16404000-16411000	Strong transcription	Adipose Nuclei	Adipose
48	chr20:16404200-16405400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr20:16404200-16405400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr20:16404200-16405400	ZNF genes & repeats	Aorta	Aorta

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