Variant report

Variant	rs7853179
Chromosome Location	chr9:100430922-100430923
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	POLR2A	chr9:100430712-100431020	K562	blood:	n/a	n/a
2	POLR2A	chr9:100430910-100431010	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:100430842-100430949	K562	blood:	n/a	n/a
4	GATA3	chr9:100430856-100431110	SH-SY5Y	brain:	n/a	chr9:100430909-100430916 chr9:100430909-100430916 chr9:100430909-100430919 chr9:100430909-100430916

No.	Distal block	Cell Line	Cell type
1	chr9:100423445..100425787-chr9:100429849..100432781,3	MCF-7	breast:
2	chr9:100428922..100431712-chr9:100433916..100435618,2	MCF-7	breast:
3	chr9:100429828..100431541-chr9:100443759..100446138,2	MCF-7	breast:
4	chr9:100426693..100428722-chr9:100429647..100432450,2	K562	blood:
5	chr9:100416541..100418307-chr9:100429425..100432057,2	MCF-7	breast:
6	chr9:100417482..100420410-chr9:100429401..100431067,2	K562	blood:
7	chr9:100401438..100403193-chr9:100429203..100431523,2	MCF-7	breast:
8	chr9:100430513..100434694-chr9:100435866..100440775,5	K562	blood:

Variant related genes	Relation type
NCBP1	TF binding region
ENSG00000136937	Chromatin interaction
ENSG00000136936	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1034098	0.81[AFR][1000 genomes]
rs1034100	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap]
rs10983030	0.95[JPT][hapmap]
rs10983035	1.00[CEU][hapmap];0.87[GIH][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs1116208	0.81[AFR][1000 genomes]
rs12375457	0.83[EUR][1000 genomes]
rs14066	0.81[AFR][1000 genomes]
rs1411344	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs1543636	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs16923041	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs16923112	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs16923269	0.86[YRI][hapmap]
rs1800975	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1928641	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs1928642	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2026132	0.95[JPT][hapmap]
rs2282066	0.81[ASW][hapmap];0.91[LWK][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes]
rs2282067	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs2297155	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2297156	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2297158	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2297159	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2297160	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2401635	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2773347	0.95[JPT][hapmap]
rs2773351	0.91[JPT][hapmap]
rs2805767	0.83[JPT][hapmap]
rs2805777	0.83[JPT][hapmap]
rs2805779	0.95[JPT][hapmap]
rs2805832	0.84[ASN][1000 genomes]
rs2805837	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2805839	0.95[JPT][hapmap]
rs2808668	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2808703	0.87[ASN][1000 genomes]
rs28403588	0.80[AFR][1000 genomes]
rs28403589	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs3176623	0.89[AFR][1000 genomes]
rs3176624	0.89[AFR][1000 genomes]
rs3176626	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176628	0.81[ASW][hapmap];0.86[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176629	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176634	0.86[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3176637	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176638	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176644	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176651	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176659	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176668	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs3176669	0.89[AFR][1000 genomes]
rs3176670	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176675	0.89[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176682	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176685	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176688	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs3176689	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3176694	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176708	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176714	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176720	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176723	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176724	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176726	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176735	0.89[AFR][1000 genomes]
rs3176736	0.89[AFR][1000 genomes]
rs3176740	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs3176744	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs3176746	0.89[AFR][1000 genomes]
rs3176747	0.89[AFR][1000 genomes]
rs3176751	0.93[YRI][hapmap]
rs3750370	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs3802472	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs3802473	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs3802474	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs41274252	0.81[AFR][1000 genomes]
rs55966848	0.83[AFR][1000 genomes]
rs56052819	0.88[AFR][1000 genomes]
rs56060429	0.83[AFR][1000 genomes]
rs56200116	0.88[AFR][1000 genomes]
rs57598118	0.89[AFR][1000 genomes]
rs58146508	0.83[AFR][1000 genomes]
rs58387091	0.81[AFR][1000 genomes]
rs58637778	0.82[AFR][1000 genomes]
rs58878935	0.84[AFR][1000 genomes]
rs59354722	0.88[AFR][1000 genomes]
rs59662386	0.84[AFR][1000 genomes]
rs59775587	0.89[AFR][1000 genomes]
rs59791764	0.83[AFR][1000 genomes]
rs59992945	0.81[AFR][1000 genomes]
rs60026475	0.82[AFR][1000 genomes]
rs60028882	0.81[AFR][1000 genomes]
rs60055057	0.84[AFR][1000 genomes]
rs60463150	0.89[AFR][1000 genomes]
rs60596698	0.81[AFR][1000 genomes]
rs60653177	0.81[AFR][1000 genomes]
rs60821994	0.89[AFR][1000 genomes]
rs61208411	0.89[AFR][1000 genomes]
rs61221847	0.84[AFR][1000 genomes]
rs61276200	0.83[AFR][1000 genomes]
rs61440789	0.88[AFR][1000 genomes]
rs61445476	0.83[AFR][1000 genomes]
rs6478304	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs7018546	0.83[AFR][1000 genomes]
rs7025403	0.80[ASW][hapmap];0.91[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs7036604	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs7045160	0.81[ASW][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7049183	0.83[AFR][1000 genomes]
rs7341850	0.81[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs73498324	0.84[AFR][1000 genomes]
rs73498332	0.84[AFR][1000 genomes]
rs73498338	0.84[AFR][1000 genomes]
rs73498347	0.84[AFR][1000 genomes]
rs73498348	0.84[AFR][1000 genomes]
rs73498355	0.84[AFR][1000 genomes]
rs73498358	0.84[AFR][1000 genomes]
rs73498362	0.84[AFR][1000 genomes]
rs73498377	0.89[AFR][1000 genomes]
rs73498380	0.89[AFR][1000 genomes]
rs73498381	0.89[AFR][1000 genomes]
rs73500325	0.89[AFR][1000 genomes]
rs73500326	0.86[AFR][1000 genomes]
rs73500328	0.89[AFR][1000 genomes]
rs73500393	0.89[AFR][1000 genomes]
rs73500395	0.89[AFR][1000 genomes]
rs73500396	0.89[AFR][1000 genomes]
rs73500397	0.89[AFR][1000 genomes]
rs73500398	0.89[AFR][1000 genomes]
rs73500400	0.89[AFR][1000 genomes]
rs73554641	0.81[AFR][1000 genomes]
rs73554646	0.81[AFR][1000 genomes]
rs73554652	0.81[AFR][1000 genomes]
rs7850986	0.89[AFR][1000 genomes]
rs7856316	0.81[AFR][1000 genomes]
rs7857174	0.85[LWK][hapmap]
rs7859684	0.81[AFR][1000 genomes]
rs7859979	0.85[LWK][hapmap]
rs7862356	0.88[AFR][1000 genomes]
rs7866961	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs7867046	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs7869683	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs9539	0.89[YRI][hapmap]
rs958346	0.95[JPT][hapmap]

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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7853179	C9orf156	cis	cerebellum	SCAN
rs7853179	XPA	cis	lymphoblastoid	seeQTL
rs7853179	TMOD1	cis	cerebellum	SCAN
rs7853179	SLC35D2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100400800-100451600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:100401200-100456000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr9:100402400-100439600	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:100402400-100451400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:100402400-100455600	Strong transcription	Dnd41	blood
6	chr9:100402600-100456000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:100402600-100456200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr9:100402800-100454200	Strong transcription	Fetal Thymus	thymus
9	chr9:100402800-100456000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:100403000-100439400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr9:100403000-100439800	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:100403000-100449400	Strong transcription	HSMM	muscle
13	chr9:100403000-100450400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr9:100403000-100454400	Strong transcription	Placenta	Placenta
15	chr9:100403000-100454600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr9:100403200-100454400	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr9:100403200-100455000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr9:100403400-100434400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:100403400-100439600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:100403400-100444200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:100403600-100453800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr9:100403800-100436200	Strong transcription	Adipose Nuclei	Adipose
23	chr9:100403800-100439000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr9:100404000-100435800	Strong transcription	A549	lung
25	chr9:100404000-100449200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:100404800-100455400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:100405000-100437800	Strong transcription	GM12878-XiMat	blood
28	chr9:100405800-100438600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr9:100409400-100439800	Strong transcription	HMEC	breast
30	chr9:100409600-100433200	Strong transcription	Fetal Intestine Large	intestine
31	chr9:100409600-100440000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:100410200-100437800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr9:100410200-100454000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr9:100411200-100451000	Strong transcription	Liver	Liver
35	chr9:100412400-100438200	Strong transcription	Fetal Muscle Leg	muscle
36	chr9:100412400-100438400	Strong transcription	Colon Smooth Muscle	Colon
37	chr9:100412400-100439000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr9:100412600-100439000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:100412600-100454200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr9:100413000-100451800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:100413400-100437800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr9:100413400-100438600	Strong transcription	Primary T cells from cord blood	blood
43	chr9:100414000-100438400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr9:100414200-100438600	Strong transcription	Brain Hippocampus Middle	brain
45	chr9:100414400-100438400	Strong transcription	Thymus	Thymus
46	chr9:100414400-100448400	Strong transcription	HUVEC	blood vessel
47	chr9:100414600-100436000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr9:100414600-100438200	Strong transcription	HSMMtube	muscle
49	chr9:100414800-100438400	Strong transcription	Left Ventricle	heart
50	chr9:100414800-100439000	Strong transcription	Osteobl	bone

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