Variant report

Variant	rs9897761
Chromosome Location	chr17:17912011-17912012
allele	A/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	TCF12	chr17:17911938-17912693	SK-N-SH	brain:	n/a	chr17:17912296-17912303 chr17:17912314-17912321
2	GATA2	chr17:17911843-17912198	SH-SY5Y	brain:	n/a	chr17:17911968-17911977
3	EP300	chr17:17911935-17912687	SK-N-SH	brain:	n/a	n/a
4	REST	chr17:17911683-17912158	SK-N-SH	brain:	n/a	n/a
5	ESR1	chr17:17911807-17912187	ECC-1	luminal epithelium:	n/a	chr17:17911973-17911990 chr17:17911974-17911991
6	TCF12	chr17:17911990-17912600	SK-N-SH	brain:	n/a	chr17:17912296-17912303 chr17:17912314-17912321
7	EP300	chr17:17911472-17913569	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:17910867..17913101-chr17:17941091..17943633,2	MCF-7	breast:
2	chr17:17910988..17913455-chr17:17916505..17918052,2	K562	blood:
3	chr17:17902979..17906251-chr17:17910368..17913208,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232344	TF binding region
ENSG00000171953	Chromatin interaction
ENSG00000201378	Chromatin interaction
ENSG00000141034	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs11078400	0.81[CEU][hapmap]
rs11078408	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11078409	0.80[AMR][1000 genomes]
rs11650021	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869491	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11870660	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11871231	0.94[EUR][1000 genomes]
rs12150369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12939020	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940282	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12941039	0.81[CEU][hapmap]
rs28537385	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28555361	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2955350	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955353	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955354	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955357	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]
rs2955358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955359	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955365	0.85[CEU][hapmap]
rs2955368	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2955369	0.82[AMR][1000 genomes]
rs2955370	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955371	0.82[CEU][hapmap]
rs2955372	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2955377	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2955378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2955380	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2955381	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2955383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955384	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2955385	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2974998	0.80[EUR][1000 genomes]
rs2974999	0.95[CEU][hapmap]
rs4072738	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4072739	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4299203	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4365348	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4368210	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4410135	0.82[EUR][1000 genomes]
rs4426402	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs4459604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4471742	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4506969	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4584886	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4643387	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924823	0.81[CEU][hapmap]
rs4924832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925133	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4925135	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4925136	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57728924	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59304093	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59518074	0.82[EUR][1000 genomes]
rs62072048	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62072049	0.84[EUR][1000 genomes]
rs62072050	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62073573	0.82[EUR][1000 genomes]
rs6502631	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502632	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502633	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6502634	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6502636	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7207461	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7207821	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7209003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7210400	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7211714	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs7212167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212447	0.95[CEU][hapmap]
rs7215524	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs721669	0.95[CEU][hapmap]
rs7219320	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7219324	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs7223696	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7224047	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7406982	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7503738	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8068175	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8069811	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8070731	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8071238	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8075189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079321	0.81[CEU][hapmap]
rs8080061	0.81[CEU][hapmap]
rs8080334	0.82[AMR][1000 genomes]
rs8080602	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8082590	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs854763	0.95[CEU][hapmap]
rs854767	0.95[CEU][hapmap]
rs854769	0.95[CEU][hapmap]
rs854790	0.95[CEU][hapmap]
rs854791	0.95[CEU][hapmap]
rs854809	0.95[CEU][hapmap]
rs854814	0.95[CEU][hapmap]
rs854817	0.95[CEU][hapmap]
rs9303144	0.95[CEU][hapmap]
rs9894138	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9896837	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9899355	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs9907246	0.81[CEU][hapmap]
rs9907287	0.81[CEU][hapmap]
rs9911850	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9912096	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914127	0.82[AMR][1000 genomes];0.84[EUR][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
rs9897761	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17876600-17914600	Weak transcription	Aorta	Aorta
2	chr17:17886800-17913000	Weak transcription	Fetal Lung	lung
3	chr17:17894000-17920600	Weak transcription	Stomach Mucosa	stomach
4	chr17:17898200-17918000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr17:17898200-17918000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr17:17898600-17917600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:17903600-17913200	Weak transcription	Gastric	stomach
8	chr17:17903600-17913600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:17906000-17914800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr17:17906200-17941400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr17:17906600-17929000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr17:17907400-17913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr17:17907400-17915800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:17907800-17915200	Strong transcription	Primary B cells from cord blood	blood
15	chr17:17908000-17913000	Weak transcription	A549	lung
16	chr17:17908000-17915400	Strong transcription	Spleen	Spleen
17	chr17:17908000-17918000	Weak transcription	Brain Germinal Matrix	brain
18	chr17:17908200-17912200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr17:17908200-17913800	Strong transcription	Fetal Stomach	stomach
20	chr17:17908200-17914200	Strong transcription	Primary T cells from cord blood	blood
21	chr17:17908200-17917600	Weak transcription	GM12878-XiMat	blood
22	chr17:17908200-17921800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr17:17908400-17912600	Strong transcription	Fetal Brain Female	brain
24	chr17:17908400-17913600	Strong transcription	Lung	lung
25	chr17:17908400-17915400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr17:17908400-17918400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr17:17908400-17928400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr17:17908600-17913000	Strong transcription	Fetal Muscle Leg	muscle
29	chr17:17908600-17932200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr17:17908800-17913200	Weak transcription	Colonic Mucosa	Colon
31	chr17:17908800-17941200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr17:17909000-17912400	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr17:17909000-17912800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr17:17909000-17913800	Strong transcription	Fetal Intestine Small	intestine
35	chr17:17909200-17912200	Strong transcription	Brain Cingulate Gyrus	brain
36	chr17:17909200-17912600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr17:17909200-17916600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr17:17909400-17915400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr17:17909400-17918800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr17:17909600-17912200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr17:17909600-17912800	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr17:17909600-17913000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr17:17909600-17916000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr17:17909600-17920800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr17:17909800-17912400	Strong transcription	Liver	Liver
46	chr17:17909800-17913800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr17:17909800-17914200	Strong transcription	Thymus	Thymus
48	chr17:17909800-17915200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr17:17910000-17915400	Strong transcription	Fetal Intestine Large	intestine
50	chr17:17910000-17916400	Strong transcription	Primary neutrophils fromperipheralblood	blood

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