Variant report

Variant	rs3001450
Chromosome Location	chr9:96085370-96085371
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	chr9:96079198..96081765-chr9:96083546..96088659,5	MCF-7	breast:
2	chr9:96082960..96085934-chr9:96086076..96089070,3	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10761203	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs10761227	1.00[YRI][hapmap]
rs10761230	1.00[YRI][hapmap]
rs10821080	0.89[CEU][hapmap];0.95[MEX][hapmap]
rs10821083	0.82[MEX][hapmap]
rs10821086	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs10821088	0.89[CEU][hapmap]
rs10821095	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs10821098	0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs10821128	1.00[YRI][hapmap]
rs10821129	1.00[YRI][hapmap]
rs10821130	1.00[YRI][hapmap]
rs10821132	1.00[YRI][hapmap]
rs10821134	1.00[YRI][hapmap]
rs10821143	1.00[YRI][hapmap]
rs10821150	1.00[YRI][hapmap]
rs10992698	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10992702	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10992751	1.00[YRI][hapmap]
rs10992769	1.00[YRI][hapmap]
rs12336667	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs12341303	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs12684394	0.83[ASN][1000 genomes]
rs1317698	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13285064	1.00[YRI][hapmap]
rs13292831	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13293217	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1539668	1.00[YRI][hapmap]
rs1544229	0.81[EUR][1000 genomes]
rs2040093	0.89[CEU][hapmap]
rs2040094	0.89[CEU][hapmap]
rs2086103	0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2306183	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2927567	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2991378	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2991379	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3001451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35795732	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3763634	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs3763635	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4743911	0.87[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4744195	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs4744201	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs4744206	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744212	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744215	0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4744242	1.00[YRI][hapmap]
rs7846729	0.81[CEU][hapmap]
rs7857039	0.91[CEU][hapmap]
rs7857937	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs7864396	1.00[YRI][hapmap]
rs7868971	0.89[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7869969	1.00[YRI][hapmap]
rs944993	0.83[EUR][1000 genomes];0.83[ASN][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	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3001450	SHC3	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96063800-96088600	Weak transcription	Right Atrium	heart
2	chr9:96067600-96086800	Weak transcription	Fetal Brain Male	brain
3	chr9:96067800-96086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:96068200-96086200	Weak transcription	Brain Anterior Caudate	brain
5	chr9:96068400-96100400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:96070600-96087800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:96074000-96088600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:96076200-96088400	Weak transcription	A549	lung
9	chr9:96079200-96088600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:96079600-96094400	Weak transcription	Stomach Mucosa	stomach
11	chr9:96080400-96087200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:96080400-96090400	Weak transcription	Gastric	stomach
13	chr9:96080800-96088000	Weak transcription	Right Ventricle	heart
14	chr9:96081000-96086200	Weak transcription	HepG2	liver
15	chr9:96081000-96100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:96081200-96088000	Weak transcription	Left Ventricle	heart
17	chr9:96081600-96088000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:96081800-96088000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:96082200-96085400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr9:96082200-96086400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:96082600-96086800	Weak transcription	Fetal Intestine Large	intestine
22	chr9:96082600-96088200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:96083200-96086800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:96083200-96087400	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:96083200-96100400	Weak transcription	Fetal Stomach	stomach
26	chr9:96083400-96094400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr9:96083800-96086200	Weak transcription	Spleen	Spleen
28	chr9:96083800-96086600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:96083800-96087000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr9:96083800-96087400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:96083800-96088400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr9:96083800-96088400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr9:96083800-96088400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:96083800-96088400	Weak transcription	Fetal Heart	heart
35	chr9:96083800-96090400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:96083800-96090800	Weak transcription	Brain Germinal Matrix	brain
37	chr9:96083800-96094400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr9:96084000-96087400	Weak transcription	Pancreas	Pancrea
39	chr9:96084600-96092400	Weak transcription	Fetal Intestine Small	intestine
40	chr9:96085200-96087800	Weak transcription	Fetal Brain Female	brain

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