Variant report

Variant	rs7021028
Chromosome Location	chr9:103317623-103317624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103316305..103318944-chr9:103319226..103321312,2	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1000477	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10465118	0.84[CHD][hapmap]
rs10465119	0.92[ASN][1000 genomes]
rs10465147	0.90[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10465148	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10465149	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs10512270	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs10512271	0.87[CHB][hapmap]
rs10819776	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap]
rs10819782	0.82[CEU][hapmap];0.94[CHB][hapmap]
rs10819785	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10819786	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10819787	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10819788	0.94[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap]
rs10819789	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10819790	0.81[ASN][1000 genomes]
rs10989082	0.80[GIH][hapmap]
rs10989094	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap]
rs10989097	0.83[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap]
rs10989103	0.94[CHB][hapmap]
rs10989104	0.81[ASN][1000 genomes]
rs10989105	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10989107	1.00[CHB][hapmap]
rs10989111	0.93[CHB][hapmap]
rs10989112	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs10989113	0.93[CHB][hapmap]
rs10989114	0.93[CHB][hapmap]
rs10989115	0.94[CHB][hapmap]
rs10989120	0.94[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap]
rs10989121	0.81[ASN][1000 genomes]
rs10989123	0.94[CHB][hapmap]
rs10989124	0.82[ASN][1000 genomes]
rs10989127	0.94[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.92[ASN][1000 genomes]
rs10989130	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10989131	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs10989134	0.81[ASN][1000 genomes]
rs10989135	0.81[ASN][1000 genomes]
rs10989140	0.89[ASN][1000 genomes]
rs10989142	0.81[ASN][1000 genomes]
rs10989143	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10989144	0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs10989145	0.94[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs10989146	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10989147	0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[ASN][1000 genomes]
rs10989150	0.88[CHB][hapmap];0.93[ASN][1000 genomes]
rs10989151	0.82[ASN][1000 genomes]
rs10989152	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989154	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989161	0.92[JPT][hapmap]
rs10989162	0.92[JPT][hapmap]
rs10989163	0.92[JPT][hapmap]
rs10989164	0.92[JPT][hapmap]
rs10989165	0.92[JPT][hapmap]
rs10989167	0.92[JPT][hapmap]
rs10989169	0.92[JPT][hapmap]
rs10989170	0.86[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs10989173	0.81[EUR][1000 genomes]
rs11793014	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12004257	0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap]
rs12056981	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs12057047	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12235981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236071	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs12236970	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12237481	0.94[CHB][hapmap]
rs12238560	0.94[CHB][hapmap]
rs12683122	0.93[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs12683548	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs12683889	0.92[JPT][hapmap]
rs12684438	0.81[CHD][hapmap]
rs12684454	0.94[CHB][hapmap]
rs13286805	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13292589	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1332598	0.94[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.92[ASN][1000 genomes]
rs16919174	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[ASN][1000 genomes]
rs16919204	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs16919211	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs1930237	0.82[ASN][1000 genomes]
rs1930246	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1931140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026423	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2069236	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2151106	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2183989	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2274881	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs2274882	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.84[ASN][1000 genomes]
rs34471402	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34816846	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4454331	0.81[EUR][1000 genomes]
rs55757829	0.82[ASN][1000 genomes]
rs55827987	1.00[ASN][1000 genomes]
rs56163523	1.00[ASN][1000 genomes]
rs56290508	0.82[ASN][1000 genomes]
rs56354846	0.82[ASN][1000 genomes]
rs59565932	0.82[ASN][1000 genomes]
rs59823190	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028822	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7029001	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7038306	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7042669	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7046659	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap]
rs7049241	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72735148	0.81[ASN][1000 genomes]
rs72735154	0.92[ASN][1000 genomes]
rs7850353	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7021028	C9orf21	cis	cerebellum	SCAN
rs7021028	C9orf125	cis	cerebellum	SCAN
rs7021028	C9orf30	cis	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103261600-103340200	Weak transcription	Left Ventricle	heart
2	chr9:103263400-103327600	Weak transcription	Aorta	Aorta
3	chr9:103273600-103337600	Weak transcription	NHDF-Ad	bronchial
4	chr9:103278400-103333000	Weak transcription	Fetal Brain Male	brain
5	chr9:103300200-103327400	Weak transcription	Ovary	ovary
6	chr9:103300800-103319800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:103307400-103323600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr9:103307400-103331800	Weak transcription	Gastric	stomach
9	chr9:103307400-103332200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:103307400-103341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr9:103307400-103347800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:103307600-103320600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:103308000-103319400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:103308000-103321400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:103308000-103321600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr9:103308000-103327200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:103308000-103340200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:103308600-103345400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:103309200-103317800	Weak transcription	NH-A	brain
20	chr9:103309400-103318000	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr9:103310000-103320600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:103311000-103328400	Weak transcription	Fetal Heart	heart
23	chr9:103311600-103330400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:103311800-103319600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:103311800-103321800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:103311800-103342400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr9:103312000-103319600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:103312000-103327200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:103312200-103328200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:103313000-103318400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr9:103313200-103340800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:103313400-103319200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:103313400-103329400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr9:103313400-103331200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:103313400-103332000	Weak transcription	Fetal Lung	lung
36	chr9:103313800-103319200	Weak transcription	HSMM	muscle
37	chr9:103314000-103323600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr9:103314800-103319000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:103316200-103318600	Enhancers	Brain Substantia Nigra	brain
40	chr9:103316400-103318800	Enhancers	Brain Hippocampus Middle	brain
41	chr9:103316400-103320000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:103316400-103323200	Weak transcription	Brain Germinal Matrix	brain
43	chr9:103316600-103318400	Enhancers	Brain Angular Gyrus	brain
44	chr9:103316600-103318400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr9:103316600-103318600	Enhancers	Brain Cingulate Gyrus	brain
46	chr9:103316600-103320000	Enhancers	HSMMtube	muscle
47	chr9:103317200-103318400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:103317200-103318800	Enhancers	GM12878-XiMat	blood
49	chr9:103317200-103320600	Strong transcription	Fetal Brain Female	brain
50	chr9:103317200-103337400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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