Variant report

Variant	rs2955382
Chromosome Location	chr17:17947710-17947711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17820370..17822488-chr17:17946052..17948620,2	K562	blood:
2	chr17:17942599..17944402-chr17:17946956..17949363,2	MCF-7	breast:
3	chr17:17942253..17945044-chr17:17945539..17948205,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171953	Chromatin interaction
ENSG00000141034	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10048206	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs1052299	0.83[CEU][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap]
rs11078400	0.91[CEU][hapmap];0.83[MEX][hapmap]
rs11078406	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs1108648	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs11650649	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs11652894	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11656840	0.81[CEU][hapmap]
rs12600546	0.82[CEU][hapmap]
rs12941039	0.91[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs12943202	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12943500	0.91[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs12943914	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12948749	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952818	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16960744	0.83[CEU][hapmap];0.84[MEX][hapmap]
rs1889014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2230316	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2350977	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs2955351	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2955360	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2955371	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744115	0.82[JPT][hapmap];0.88[MEX][hapmap]
rs4077828	0.82[CEU][hapmap]
rs4244602	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs4257260	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs4321247	0.91[ASN][1000 genomes]
rs4341796	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs4413022	0.82[CEU][hapmap]
rs4459604	0.80[MEX][hapmap]
rs4470201	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs4924822	0.82[JPT][hapmap];0.83[MEX][hapmap]
rs4924823	0.91[CEU][hapmap];0.84[MEX][hapmap]
rs4925120	0.83[CEU][hapmap];0.84[MEX][hapmap]
rs4925123	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs4925125	0.84[MEX][hapmap]
rs4925126	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs4925129	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs4925130	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs4925138	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5002487	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs62072049	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6502619	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6502622	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs6502624	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs6502625	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs6502627	0.82[CEU][hapmap]
rs6502629	0.91[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs712265	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7207395	1.00[JPT][hapmap]
rs7213225	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs7214002	0.82[CEU][hapmap]
rs7222480	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs7224815	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs72827413	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7501812	0.82[JPT][hapmap];0.87[MEX][hapmap]
rs7503334	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs8065416	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs8065563	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs8066982	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs8070128	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs8070748	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs8073001	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs8077338	0.81[EUR][1000 genomes]
rs8078105	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs8078138	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs8078583	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs8079321	0.91[CEU][hapmap];0.84[MEX][hapmap]
rs8079418	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8080061	0.91[CEU][hapmap];0.84[MEX][hapmap]
rs8080823	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs854762	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs854764	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs854765	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs854766	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs854810	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs854813	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs950966	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs9890341	0.82[CEU][hapmap]
rs9907246	0.91[CEU][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap]
rs9907287	0.91[CEU][hapmap];0.84[MEX][hapmap]
rs9912895	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs9913277	0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS 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 miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2955382	DRG2	cis	Thyroid	GTEx
rs2955382	TOM1L2	cis	parietal	SCAN
rs2955382	SREBF1	cis	Whole Blood	GTEx
rs2955382	TOM1L2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17944000-17948200	Weak transcription	Aorta	Aorta
2	chr17:17944000-17948200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr17:17944000-17974200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:17944000-17974200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr17:17944200-17948000	Weak transcription	Thymus	Thymus
6	chr17:17944200-17948400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr17:17944200-17948400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr17:17944200-17948400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr17:17944200-17948600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr17:17944200-17950400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr17:17944200-17956000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr17:17944200-17957200	Weak transcription	NH-A	brain
13	chr17:17944200-17957400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr17:17944200-17957400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr17:17944200-17974400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr17:17944400-17948200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr17:17944400-17948400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr17:17944400-17948600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:17944400-17948800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr17:17944400-17948800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:17944400-17948800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:17944400-17949400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:17944400-17949400	Weak transcription	Colonic Mucosa	Colon
24	chr17:17944400-17949400	Weak transcription	Fetal Intestine Large	intestine
25	chr17:17944400-17949400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:17944400-17949600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:17944400-17950600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr17:17944400-17957200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr17:17944400-17957200	Weak transcription	Gastric	stomach
30	chr17:17944400-17957200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr17:17944400-17957600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr17:17944400-17961800	Weak transcription	Fetal Kidney	kidney
33	chr17:17944400-17962000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr17:17944400-17978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:17944600-17957200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr17:17944800-17950200	Weak transcription	A549	lung
37	chr17:17944800-17950400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr17:17945000-17948000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr17:17945000-17957000	Weak transcription	Fetal Lung	lung
40	chr17:17945000-17957400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr17:17945000-17960000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:17945200-17947800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr17:17945200-17948000	Weak transcription	Primary B cells from cord blood	blood
44	chr17:17945200-17948200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr17:17945200-17948400	Weak transcription	Lung	lung
46	chr17:17945200-17948800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr17:17945200-17949000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr17:17945200-17949000	Weak transcription	Right Ventricle	heart
49	chr17:17945200-17949200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr17:17945200-17949400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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