Variant report

Variant	rs7859979
Chromosome Location	chr9:100365510-100365511
allele	G/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	POLR2A	chr9:100364009-100365556	K562	blood:	n/a	n/a
2	POLR2A	chr9:100365376-100365549	K562	blood:	n/a	n/a
3	POLR2A	chr9:100360719-100370063	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100364434..100366925-chr9:100393876..100396589,2	MCF-7	breast:
2	chr9:100361363..100362991-chr9:100365453..100368100,2	MCF-7	breast:

Variant related genes	Relation type
TSTD2	TF binding region
ENSG00000136937	Chromatin interaction
ENSG00000136925	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1034098	0.86[AFR][1000 genomes]
rs1034100	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.86[MKK][hapmap]
rs1116208	0.86[AFR][1000 genomes]
rs14066	0.86[AFR][1000 genomes]
rs1411344	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.86[AFR][1000 genomes]
rs1543636	0.86[AFR][1000 genomes]
rs16923033	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16923041	0.82[AFR][1000 genomes]
rs16923112	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap]
rs1813875	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1928641	0.86[AFR][1000 genomes]
rs1928642	0.86[AFR][1000 genomes]
rs2282066	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.85[AFR][1000 genomes]
rs2282067	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.86[AFR][1000 genomes]
rs28403588	0.83[AFR][1000 genomes]
rs28403589	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.84[AFR][1000 genomes]
rs3176626	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap]
rs3176628	0.93[ASW][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap]
rs3176629	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap]
rs3176634	0.87[ASW][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap]
rs3176635	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs3176657	0.88[AFR][1000 genomes]
rs3176668	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap]
rs3176675	0.85[YRI][hapmap]
rs3176687	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3176694	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap]
rs3176706	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3176708	0.82[YRI][hapmap]
rs3176711	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3176712	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3176740	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap]
rs3176744	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap]
rs3750370	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.86[AFR][1000 genomes]
rs3802472	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.86[AFR][1000 genomes]
rs3802473	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.86[AFR][1000 genomes]
rs3802474	0.81[AFR][1000 genomes]
rs41274252	0.86[AFR][1000 genomes]
rs55966848	0.86[AFR][1000 genomes]
rs56060429	0.86[AFR][1000 genomes]
rs58146508	0.82[AFR][1000 genomes]
rs58387091	0.86[AFR][1000 genomes]
rs58390229	0.83[AFR][1000 genomes]
rs58637778	0.86[AFR][1000 genomes]
rs58878935	0.84[AFR][1000 genomes]
rs59478543	0.84[AFR][1000 genomes]
rs59662386	0.82[AFR][1000 genomes]
rs59791764	0.86[AFR][1000 genomes]
rs59992945	0.86[AFR][1000 genomes]
rs60026475	0.85[AFR][1000 genomes]
rs60028882	0.86[AFR][1000 genomes]
rs60055057	0.82[AFR][1000 genomes]
rs60596698	0.86[AFR][1000 genomes]
rs60653177	0.86[AFR][1000 genomes]
rs61221847	0.82[AFR][1000 genomes]
rs61276200	0.86[AFR][1000 genomes]
rs61445476	0.86[AFR][1000 genomes]
rs61739366	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6478304	0.86[AFR][1000 genomes]
rs6478305	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7018546	0.86[AFR][1000 genomes]
rs7021377	0.90[AFR][1000 genomes]
rs7025403	0.93[ASW][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.86[AFR][1000 genomes]
rs7036604	0.85[AFR][1000 genomes]
rs7045160	0.93[ASW][hapmap];0.87[GIH][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap]
rs7049183	0.86[AFR][1000 genomes]
rs7341850	0.93[ASW][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.82[AFR][1000 genomes]
rs73498323	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498324	0.84[AFR][1000 genomes]
rs73498329	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498332	0.82[AFR][1000 genomes]
rs73498338	0.82[AFR][1000 genomes]
rs73498347	0.82[AFR][1000 genomes]
rs73498348	0.82[AFR][1000 genomes]
rs73498355	0.82[AFR][1000 genomes]
rs73498358	0.82[AFR][1000 genomes]
rs73498359	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73498362	0.82[AFR][1000 genomes]
rs73498365	0.90[AFR][1000 genomes]
rs73500307	0.89[AFR][1000 genomes]
rs73500321	0.90[AFR][1000 genomes]
rs73500392	0.89[AFR][1000 genomes]
rs73502208	0.88[AFR][1000 genomes]
rs73502210	0.88[AFR][1000 genomes]
rs73551090	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73552520	0.84[AFR][1000 genomes]
rs73554631	0.84[AFR][1000 genomes]
rs73554641	0.86[AFR][1000 genomes]
rs73554646	0.86[AFR][1000 genomes]
rs73554650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73554652	0.86[AFR][1000 genomes]
rs7853179	0.85[LWK][hapmap]
rs7856316	0.86[AFR][1000 genomes]
rs7857174	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7859684	0.86[AFR][1000 genomes]
rs7866961	0.82[AFR][1000 genomes]
rs7867046	0.86[AFR][1000 genomes]
rs7869683	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7859979	TSTD2	cis	lymphoblastoid	seeQTL
rs7859979	XPA	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100348800-100384000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:100361000-100367200	Weak transcription	Small Intestine	intestine
3	chr9:100361000-100381200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:100361200-100366600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr9:100361200-100366600	Weak transcription	NH-A	brain
6	chr9:100361200-100368400	Strong transcription	Brain Anterior Caudate	brain
7	chr9:100361400-100368600	Strong transcription	Hela-S3	cervix
8	chr9:100361400-100370000	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:100361600-100366400	Weak transcription	NHDF-Ad	bronchial
10	chr9:100361600-100368400	Strong transcription	Stomach Smooth Muscle	stomach
11	chr9:100361600-100369000	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:100361600-100369200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr9:100361600-100369400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr9:100361600-100369800	Strong transcription	Dnd41	blood
15	chr9:100361600-100370200	Strong transcription	Brain Hippocampus Middle	brain
16	chr9:100361600-100371000	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr9:100361600-100371200	Strong transcription	Liver	Liver
18	chr9:100361600-100371400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:100361600-100371600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:100361600-100375800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr9:100361800-100365600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr9:100361800-100368400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:100361800-100368400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:100361800-100369000	Strong transcription	Ovary	ovary
25	chr9:100361800-100369200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:100361800-100369400	Strong transcription	Brain Cingulate Gyrus	brain
27	chr9:100361800-100369800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr9:100361800-100370800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:100361800-100371200	Strong transcription	Placenta	Placenta
30	chr9:100361800-100371200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr9:100361800-100371400	Strong transcription	Primary B cells from cord blood	blood
32	chr9:100361800-100371400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:100361800-100371400	Strong transcription	Fetal Stomach	stomach
34	chr9:100361800-100371400	Strong transcription	Lung	lung
35	chr9:100361800-100374000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr9:100361800-100374400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr9:100361800-100375800	Strong transcription	Primary T cells from cord blood	blood
38	chr9:100361800-100376000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:100361800-100376000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr9:100361800-100376000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr9:100361800-100376000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr9:100361800-100383400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:100361800-100389000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:100361800-100394000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr9:100362000-100369000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr9:100362000-100369800	Strong transcription	Fetal Lung	lung
47	chr9:100362000-100370000	Strong transcription	Fetal Intestine Large	intestine
48	chr9:100362200-100369200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr9:100362200-100373800	Weak transcription	Fetal Brain Male	brain
50	chr9:100362200-100379000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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