Variant report

Variant	rs2955357
Chromosome Location	chr17:17946401-17946402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr17:17946298-17946661	K562	blood:	n/a	chr17:17946464-17946473 chr17:17946462-17946475 chr17:17946463-17946474 chr17:17946464-17946471 chr17:17946463-17946474
2	BHLHE40	chr17:17946319-17946660	K562	blood:	n/a	n/a
3	MAX	chr17:17946309-17946606	K562	blood:	n/a	chr17:17946464-17946473 chr17:17946462-17946475 chr17:17946463-17946474 chr17:17946464-17946471 chr17:17946463-17946474
4	TAL1	chr17:17946380-17946640	K562	blood:	n/a	chr17:17946474-17946482
5	MYC	chr17:17946338-17946665	K562	blood:	n/a	chr17:17946464-17946473 chr17:17946462-17946475 chr17:17946463-17946474 chr17:17946464-17946471 chr17:17946463-17946474
6	MXI1	chr17:17946299-17946571	K562	blood:	n/a	n/a
7	MAX	chr17:17946295-17946604	K562	blood:	n/a	chr17:17946464-17946473 chr17:17946462-17946475 chr17:17946463-17946474 chr17:17946464-17946471 chr17:17946463-17946474
8	E2F6	chr17:17946356-17946553	K562	blood:	n/a	n/a
9	GATA1	chr17:17946110-17947095	PBDE	blood:	n/a	chr17:17947076-17947083
10	JUND	chr17:17946334-17946540	K562	blood:	n/a	n/a
11	USF1	chr17:17946338-17946634	K562	blood:	n/a	n/a
12	MAX	chr17:17946281-17946632	K562	blood:	n/a	chr17:17946464-17946473 chr17:17946462-17946475 chr17:17946463-17946474 chr17:17946464-17946471 chr17:17946463-17946474

No.	Distal block	Cell Line	Cell type
1	chr17:17944377..17946429-chr17:17996253..17997823,2	K562	blood:
2	chr17:17942903..17946429-chr17:17996253..17997904,3	K562	blood:
3	chr17:17820370..17822488-chr17:17946052..17948620,2	K562	blood:
4	chr17:17943464..17946446-chr17:17950718..17954584,5	K562	blood:
5	chr17:17740231..17742175-chr17:17944885..17946764,2	MCF-7	breast:
6	chr17:17942253..17945044-chr17:17945539..17948205,4	MCF-7	breast:

Variant related genes	Relation type
ATPAF2	TF binding region
ENSG00000141034	Chromatin interaction
ENSG00000171953	Chromatin interaction
ENSG00000072310	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1008135	0.83[EUR][1000 genomes]
rs1101727	0.83[EUR][1000 genomes]
rs11078408	0.90[CEU][hapmap]
rs11078410	0.82[EUR][1000 genomes]
rs11650021	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658257	0.81[AMR][1000 genomes]
rs11869491	0.86[EUR][1000 genomes]
rs11870660	0.90[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11871231	0.87[EUR][1000 genomes]
rs12150369	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12939020	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940282	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12948749	0.84[EUR][1000 genomes]
rs2056842	0.82[EUR][1000 genomes]
rs28537385	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28555361	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2955350	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2955352	0.82[AMR][1000 genomes]
rs2955353	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2955354	1.00[CEU][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2955355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955359	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2955365	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955366	0.83[EUR][1000 genomes]
rs2955368	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2955369	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2955370	1.00[CEU][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2955371	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955372	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2955373	0.82[AMR][1000 genomes]
rs2955377	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2955378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2955380	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2955381	1.00[CEU][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2955383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955384	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2955385	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2974998	0.86[EUR][1000 genomes]
rs2974999	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs4072738	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs4072739	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs4299203	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4365346	0.85[EUR][1000 genomes]
rs4365348	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4368210	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4410135	0.87[EUR][1000 genomes]
rs4426402	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs4459604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4506967	0.81[EUR][1000 genomes]
rs4506969	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4561528	0.84[EUR][1000 genomes]
rs4584886	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4643387	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925135	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4925136	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57728924	0.83[ASN][1000 genomes]
rs59304093	0.81[ASN][1000 genomes]
rs59518074	0.87[EUR][1000 genomes]
rs62072048	0.83[EUR][1000 genomes]
rs62072050	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62073573	0.87[EUR][1000 genomes]
rs6502631	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502632	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502633	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6502634	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6502636	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6502637	0.85[EUR][1000 genomes]
rs6826	0.83[EUR][1000 genomes]
rs712267	0.83[EUR][1000 genomes]
rs712268	0.83[EUR][1000 genomes]
rs7207461	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7207821	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7209003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7210400	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7211714	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7212167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212447	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7215524	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs721669	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs7219320	0.82[CEU][hapmap];0.81[ASN][1000 genomes]
rs7219324	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs7223696	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7224047	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7406744	0.85[EUR][1000 genomes]
rs7406982	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs741782	0.83[EUR][1000 genomes]
rs7503738	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8066764	0.85[EUR][1000 genomes]
rs8068175	0.90[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8069811	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070731	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8071238	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8075189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080334	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8080602	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8082590	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs854763	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs854767	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs854768	0.83[EUR][1000 genomes]
rs854769	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs854770	0.83[EUR][1000 genomes]
rs854789	0.83[EUR][1000 genomes]
rs854790	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs854791	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs854808	0.83[EUR][1000 genomes]
rs854809	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs854814	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs854817	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs854818	0.82[EUR][1000 genomes]
rs9303144	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs9894138	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9896837	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9897761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9899355	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9911850	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9912096	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2955357	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17943800-17946600	Enhancers	Fetal Brain Male	brain
2	chr17:17944000-17948200	Weak transcription	Aorta	Aorta
3	chr17:17944000-17948200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:17944000-17974200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr17:17944000-17974200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr17:17944200-17947000	Enhancers	Fetal Heart	heart
7	chr17:17944200-17947000	Enhancers	Psoas Muscle	Psoas
8	chr17:17944200-17947400	Weak transcription	Fetal Intestine Small	intestine
9	chr17:17944200-17948000	Weak transcription	Thymus	Thymus
10	chr17:17944200-17948400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr17:17944200-17948400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr17:17944200-17948400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr17:17944200-17948600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr17:17944200-17950400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:17944200-17956000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr17:17944200-17957200	Weak transcription	NH-A	brain
17	chr17:17944200-17957400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr17:17944200-17957400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr17:17944200-17974400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr17:17944400-17946600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr17:17944400-17947000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:17944400-17947200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:17944400-17947400	Weak transcription	Primary T cells from cord blood	blood
24	chr17:17944400-17947400	Weak transcription	Fetal Stomach	stomach
25	chr17:17944400-17948200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr17:17944400-17948400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:17944400-17948600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:17944400-17948800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr17:17944400-17948800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr17:17944400-17948800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr17:17944400-17949400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:17944400-17949400	Weak transcription	Colonic Mucosa	Colon
33	chr17:17944400-17949400	Weak transcription	Fetal Intestine Large	intestine
34	chr17:17944400-17949400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr17:17944400-17949600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr17:17944400-17950600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr17:17944400-17957200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr17:17944400-17957200	Weak transcription	Gastric	stomach
39	chr17:17944400-17957200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr17:17944400-17957600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr17:17944400-17961800	Weak transcription	Fetal Kidney	kidney
42	chr17:17944400-17962000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr17:17944400-17978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:17944600-17946600	Enhancers	Fetal Brain Female	brain
45	chr17:17944600-17946800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr17:17944600-17947000	Enhancers	HepG2	liver
47	chr17:17944600-17947400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr17:17944600-17957200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:17944800-17950200	Weak transcription	A549	lung
50	chr17:17944800-17950400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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