Variant report

Variant	rs10978196
Chromosome Location	chr9:108441914-108441915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108438804..108448538-chr9:108453257..108460732,10	K562	blood:
2	chr9:108437211..108439069-chr9:108439527..108442276,2	MCF-7	breast:
3	chr9:108434094..108435795-chr9:108440059..108442586,2	MCF-7	breast:
4	chr9:108441575..108443928-chr9:108443959..108447261,3	MCF-7	breast:
5	chr9:108432330..108435040-chr9:108440463..108442101,2	K562	blood:

Variant related genes	Relation type
ENSG00000095209	Chromatin interaction

Extended variants
information (count: 202 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:200)

rs_ID	r²[population]
rs10046892	0.86[ASN][1000 genomes]
rs10114077	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10114109	0.86[ASN][1000 genomes]
rs10114738	0.86[ASN][1000 genomes]
rs10114831	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10115748	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10115852	0.85[ASN][1000 genomes]
rs10116270	0.86[ASN][1000 genomes]
rs10117187	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10118661	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10119128	0.87[ASN][1000 genomes]
rs10121582	0.86[ASN][1000 genomes]
rs10121677	0.83[ASN][1000 genomes]
rs10121695	0.82[ASN][1000 genomes]
rs10122308	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10123642	0.83[ASN][1000 genomes]
rs10124738	0.85[ASN][1000 genomes]
rs10125298	0.83[ASN][1000 genomes]
rs10125446	0.86[ASN][1000 genomes]
rs10156569	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10156571	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10217358	0.83[ASN][1000 genomes]
rs10217508	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10441744	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10512340	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10739213	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10759128	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10759132	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10759133	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10759134	0.86[ASN][1000 genomes]
rs10759135	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759136	0.85[ASN][1000 genomes]
rs10759137	0.83[ASN][1000 genomes]
rs10759138	0.83[ASN][1000 genomes]
rs10816294	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816295	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816296	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10816297	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816298	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10816299	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10816300	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10816301	0.86[ASN][1000 genomes]
rs10816302	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10816304	0.86[ASN][1000 genomes]
rs10816308	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10816310	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10816311	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10816312	0.86[ASN][1000 genomes]
rs10816313	0.91[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10816314	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10816318	0.86[ASN][1000 genomes]
rs10816319	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10816324	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10816330	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10816331	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10816334	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10816336	0.82[ASN][1000 genomes]
rs10816337	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10978198	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10978202	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978203	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978209	0.89[ASN][1000 genomes]
rs10978210	0.89[ASN][1000 genomes]
rs10978211	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10978220	0.91[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10978222	0.86[ASN][1000 genomes]
rs10978223	0.86[ASN][1000 genomes]
rs10978226	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10978227	0.86[ASN][1000 genomes]
rs10978228	0.86[ASN][1000 genomes]
rs10978230	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10978232	0.83[ASN][1000 genomes]
rs10978233	0.84[ASN][1000 genomes]
rs10978234	0.86[ASN][1000 genomes]
rs10978235	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10978236	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10978239	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10978240	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10978241	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10978242	0.83[ASN][1000 genomes]
rs10978251	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10978252	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10978253	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10978255	0.83[ASN][1000 genomes]
rs10978257	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10978259	0.83[ASN][1000 genomes]
rs10978263	0.83[ASN][1000 genomes]
rs10978264	0.83[ASN][1000 genomes]
rs10978265	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10978267	0.83[ASN][1000 genomes]
rs1124097	0.97[ASN][1000 genomes]
rs11532966	0.82[ASN][1000 genomes]
rs11562290	0.83[ASN][1000 genomes]
rs12001759	0.85[ASN][1000 genomes]
rs12003526	0.85[ASN][1000 genomes]
rs12337178	0.86[ASN][1000 genomes]
rs12338812	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12338851	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12339468	0.83[ASN][1000 genomes]
rs12341846	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12341885	0.85[ASN][1000 genomes]
rs12342953	0.85[ASN][1000 genomes]
rs12344129	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12344225	0.83[ASN][1000 genomes]
rs12345343	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12346348	0.86[ASN][1000 genomes]
rs12347783	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12347903	0.95[ASN][1000 genomes]
rs12348107	0.83[ASN][1000 genomes]
rs12684672	0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13283916	0.82[ASN][1000 genomes]
rs13286237	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs13301124	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1979992	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1979993	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2136406	0.84[ASN][1000 genomes]
rs2136407	0.83[ASN][1000 genomes]
rs2136408	0.86[ASN][1000 genomes]
rs2136410	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2175121	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2175122	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2271246	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28579191	0.89[ASN][1000 genomes]
rs35164306	0.86[ASN][1000 genomes]
rs3817141	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4360347	0.83[ASN][1000 genomes]
rs6477453	0.86[ASN][1000 genomes]
rs6477454	0.86[ASN][1000 genomes]
rs6477455	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6477456	0.86[ASN][1000 genomes]
rs6477457	0.85[ASN][1000 genomes]
rs6477459	0.86[ASN][1000 genomes]
rs6477460	0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6477462	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6477463	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6477464	0.86[ASN][1000 genomes]
rs6477466	0.82[ASN][1000 genomes]
rs66993159	0.83[ASN][1000 genomes]
rs67705477	0.83[ASN][1000 genomes]
rs7020276	0.86[ASN][1000 genomes]
rs7020523	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7021342	0.82[ASN][1000 genomes]
rs7021727	0.83[ASN][1000 genomes]
rs7022124	0.86[ASN][1000 genomes]
rs7024278	0.86[ASN][1000 genomes]
rs7025950	0.87[ASN][1000 genomes]
rs7026814	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7026968	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7028906	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7029064	0.84[ASN][1000 genomes]
rs7029124	0.87[ASN][1000 genomes]
rs7029200	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7030399	0.85[ASN][1000 genomes]
rs7030619	0.89[ASN][1000 genomes]
rs7031063	0.86[ASN][1000 genomes]
rs7031360	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7031431	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7037785	0.84[ASN][1000 genomes]
rs7038788	0.86[ASN][1000 genomes]
rs7040532	0.86[ASN][1000 genomes]
rs7040890	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7046212	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7046293	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7046947	0.83[ASN][1000 genomes]
rs7047435	0.86[ASN][1000 genomes]
rs7047678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73522059	0.83[ASN][1000 genomes]
rs7846853	0.86[ASN][1000 genomes]
rs7846993	0.86[ASN][1000 genomes]
rs7848176	0.86[ASN][1000 genomes]
rs7852501	0.83[ASN][1000 genomes]
rs7853483	0.80[ASN][1000 genomes]
rs7854472	0.83[ASN][1000 genomes]
rs7856126	0.85[ASN][1000 genomes]
rs7856356	0.82[ASN][1000 genomes]
rs7858409	0.85[ASN][1000 genomes]
rs7858663	0.86[ASN][1000 genomes]
rs7861670	0.86[ASN][1000 genomes]
rs7862792	0.81[EUR][1000 genomes]
rs7862921	0.83[ASN][1000 genomes]
rs7866285	0.84[ASN][1000 genomes]
rs7867049	0.85[ASN][1000 genomes]
rs7867239	0.83[ASN][1000 genomes]
rs7867503	0.83[ASN][1000 genomes]
rs7867973	0.86[ASN][1000 genomes]
rs7869654	0.83[ASN][1000 genomes]
rs7871299	0.86[ASN][1000 genomes]
rs7871452	0.86[ASN][1000 genomes]
rs7873663	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7874069	0.85[ASN][1000 genomes]
rs7875434	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9696294	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9696296	0.82[ASN][1000 genomes]
rs9777628	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9969715	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9969789	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9987409	0.83[ASN][1000 genomes]
rs9987489	0.83[ASN][1000 genomes]
rs9987692	0.83[ASN][1000 genomes]
rs9987932	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519023	chr9:108371549-108454745	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	n/a
2	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10978196	TMEM38B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108423600-108451600	Weak transcription	Psoas Muscle	Psoas
2	chr9:108439600-108442000	Weak transcription	K562	blood
3	chr9:108440000-108442200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:108440200-108442000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr9:108440200-108442000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr9:108440200-108443000	Enhancers	Liver	Liver
7	chr9:108441000-108445600	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:108441400-108442000	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr9:108441400-108442200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr9:108441400-108445800	Weak transcription	HSMMtube	muscle
11	chr9:108441600-108442200	Flanking Active TSS	HepG2	liver
12	chr9:108441800-108442000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:108441800-108442000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:108441800-108442000	Enhancers	Fetal Kidney	kidney
15	chr9:108441800-108442200	Active TSS	Rectal Mucosa Donor 29	rectum

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