Variant report

Variant	rs7046659
Chromosome Location	chr9:103211325-103211326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103200752..103203739-chr9:103209963..103212371,2	K562	blood:
2	chr9:103206264..103208362-chr9:103209837..103212549,2	MCF-7	breast:
3	chr9:103188382..103190819-chr9:103209723..103211869,2	MCF-7	breast:
4	chr9:103209511..103211165-chr9:103211281..103213685,2	K562	blood:

Variant related genes	Relation type
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 180 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:177)

rs_ID	r²[population]
rs1000477	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1016176	0.81[EUR][1000 genomes]
rs1016177	0.81[EUR][1000 genomes]
rs1041565	0.97[ASN][1000 genomes]
rs10465118	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10465145	0.89[ASN][1000 genomes]
rs10465147	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10465148	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs10465149	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10512270	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10512271	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10819773	1.00[JPT][hapmap]
rs10819774	0.81[CHB][hapmap];0.89[ASN][1000 genomes]
rs10819775	0.89[ASN][1000 genomes]
rs10819776	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10819779	0.98[ASN][1000 genomes]
rs10819781	1.00[ASN][1000 genomes]
rs10819782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10819785	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs10819786	0.97[ASN][1000 genomes]
rs10819787	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10819788	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[ASN][1000 genomes]
rs10819789	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs10819790	0.83[ASN][1000 genomes]
rs10989078	1.00[JPT][hapmap]
rs10989081	1.00[JPT][hapmap]
rs10989082	0.82[ASW][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10989085	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989090	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10989091	0.97[ASN][1000 genomes]
rs10989092	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10989093	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10989094	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10989095	0.98[ASN][1000 genomes]
rs10989097	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10989099	1.00[ASN][1000 genomes]
rs10989103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989108	0.97[ASN][1000 genomes]
rs10989111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989112	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989120	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989121	0.89[ASN][1000 genomes]
rs10989123	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989124	0.84[ASN][1000 genomes]
rs10989127	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs10989130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10989131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10989134	0.83[ASN][1000 genomes]
rs10989135	0.83[ASN][1000 genomes]
rs10989142	0.83[ASN][1000 genomes]
rs10989143	0.83[ASN][1000 genomes]
rs10989144	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10989145	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10989146	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10989147	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs10989150	0.94[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs10989151	0.82[ASN][1000 genomes]
rs10989152	0.87[CHB][hapmap]
rs10989153	0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap]
rs10989154	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs10989156	0.94[CHB][hapmap]
rs10989161	0.82[JPT][hapmap]
rs10989162	0.82[JPT][hapmap]
rs10989163	0.82[JPT][hapmap]
rs10989164	0.82[JPT][hapmap]
rs10989165	0.82[JPT][hapmap]
rs10989167	0.82[JPT][hapmap]
rs10989169	0.82[JPT][hapmap]
rs10989170	0.82[JPT][hapmap]
rs11793014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs12004257	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12005378	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12056981	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12057047	0.97[ASN][1000 genomes]
rs12235981	0.94[CHB][hapmap]
rs12236071	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12236952	0.97[ASN][1000 genomes]
rs12236970	0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap]
rs12237166	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12237481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12238560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12682741	1.00[ASN][1000 genomes]
rs12683122	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12683548	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12683889	0.82[JPT][hapmap]
rs12684438	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12684454	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13286805	0.97[ASN][1000 genomes]
rs13292589	0.97[ASN][1000 genomes]
rs1332598	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs16919136	0.97[ASN][1000 genomes]
rs16919174	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16919204	0.81[JPT][hapmap]
rs16919211	0.82[JPT][hapmap]
rs17741842	0.81[MEX][hapmap]
rs17813663	0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs17813801	0.87[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs17813854	0.80[EUR][1000 genomes]
rs17814768	0.81[MEX][hapmap]
rs1930237	0.84[ASN][1000 genomes]
rs1930238	0.81[MEX][hapmap]
rs1930245	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1930246	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs1931140	0.94[CHB][hapmap]
rs2026423	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2026998	0.87[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs2069236	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2151106	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2183989	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2183990	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs2183991	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs2274881	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2274882	0.80[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[ASN][1000 genomes]
rs2780958	0.81[YRI][hapmap]
rs34471402	0.97[ASN][1000 genomes]
rs35438121	0.82[EUR][1000 genomes]
rs41274963	0.82[EUR][1000 genomes]
rs4395949	0.80[EUR][1000 genomes]
rs56012200	0.83[ASN][1000 genomes]
rs56020062	0.83[ASN][1000 genomes]
rs56050588	0.85[ASN][1000 genomes]
rs56122790	0.89[ASN][1000 genomes]
rs56170030	0.97[ASN][1000 genomes]
rs56313595	0.81[EUR][1000 genomes]
rs56720423	0.80[EUR][1000 genomes]
rs57241635	0.81[EUR][1000 genomes]
rs58030694	0.81[EUR][1000 genomes]
rs58698990	0.80[EUR][1000 genomes]
rs59565932	0.84[ASN][1000 genomes]
rs59611728	0.96[ASN][1000 genomes]
rs61306839	0.82[EUR][1000 genomes]
rs61386923	0.81[EUR][1000 genomes]
rs7021028	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap]
rs7024666	1.00[ASN][1000 genomes]
rs7028822	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs7029001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7031884	0.90[JPT][hapmap];0.81[YRI][hapmap]
rs7034154	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041189	0.81[MEX][hapmap]
rs7041933	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7049241	0.97[ASN][1000 genomes]
rs72735107	0.89[ASN][1000 genomes]
rs72735110	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72735119	0.98[ASN][1000 genomes]
rs72735122	0.98[ASN][1000 genomes]
rs72735140	0.97[ASN][1000 genomes]
rs72735148	0.89[ASN][1000 genomes]
rs73655530	0.80[EUR][1000 genomes]
rs73655531	0.80[EUR][1000 genomes]
rs73655532	0.80[EUR][1000 genomes]
rs73655533	0.80[EUR][1000 genomes]
rs73655534	0.80[EUR][1000 genomes]
rs73655535	0.80[EUR][1000 genomes]
rs73655536	0.80[EUR][1000 genomes]
rs73655537	0.80[EUR][1000 genomes]
rs73655539	0.81[EUR][1000 genomes]
rs73655540	0.81[EUR][1000 genomes]
rs73655541	0.81[EUR][1000 genomes]
rs73655542	0.81[EUR][1000 genomes]
rs73655543	0.81[EUR][1000 genomes]
rs73655544	0.81[EUR][1000 genomes]
rs73655545	0.81[EUR][1000 genomes]
rs73655546	0.81[EUR][1000 genomes]
rs73655547	0.81[EUR][1000 genomes]
rs73655549	0.82[EUR][1000 genomes]
rs73655550	0.82[EUR][1000 genomes]
rs73655551	0.80[EUR][1000 genomes]
rs73655553	0.80[EUR][1000 genomes]
rs73655554	0.80[EUR][1000 genomes]
rs7865385	0.81[MEX][hapmap]
rs7869933	1.00[ASN][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	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7046659	C9orf30	Cis_1M	lymphoblastoid	RTeQTL
rs7046659	C9orf30	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103190400-103214200	Weak transcription	Thymus	Thymus
2	chr9:103190600-103214400	Weak transcription	Primary B cells from cord blood	blood
3	chr9:103190600-103224600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:103190800-103213200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:103190800-103217600	Weak transcription	Fetal Intestine Large	intestine
6	chr9:103191200-103214200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:103191600-103212800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:103191600-103213000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:103191600-103214400	Weak transcription	Esophagus	oesophagus
10	chr9:103191800-103217600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr9:103191800-103228000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:103192000-103214000	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:103192600-103213200	Weak transcription	Fetal Brain Male	brain
14	chr9:103193000-103214400	Weak transcription	Pancreas	Pancrea
15	chr9:103194600-103213200	Weak transcription	Lung	lung
16	chr9:103196200-103226400	Weak transcription	Psoas Muscle	Psoas
17	chr9:103197200-103211600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:103200000-103217000	Weak transcription	K562	blood
19	chr9:103201200-103215600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr9:103201600-103215400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:103202000-103213400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:103202000-103215800	Weak transcription	Fetal Thymus	thymus
23	chr9:103202600-103213800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:103202800-103217400	Weak transcription	Right Ventricle	heart
25	chr9:103203800-103215600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:103203800-103217400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:103204000-103214000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:103204000-103216800	Strong transcription	Osteobl	bone
29	chr9:103204200-103214000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:103204400-103212600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:103204600-103221200	Weak transcription	Fetal Kidney	kidney
32	chr9:103204800-103212800	Weak transcription	Adipose Nuclei	Adipose
33	chr9:103204800-103213200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:103204800-103213200	Weak transcription	Placenta	Placenta
35	chr9:103205000-103213000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr9:103205000-103213600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr9:103205000-103214200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:103205000-103214400	Weak transcription	Gastric	stomach
39	chr9:103205000-103216800	Weak transcription	Fetal Intestine Small	intestine
40	chr9:103206000-103217000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr9:103206200-103212800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr9:103206200-103212800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr9:103206800-103213000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr9:103206800-103213200	Weak transcription	Fetal Brain Female	brain
45	chr9:103206800-103213800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr9:103206800-103214000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr9:103206800-103216200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr9:103206800-103217000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr9:103207000-103212800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr9:103207000-103212800	Weak transcription	Primary T cells fromperipheralblood	blood

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