Variant report

Variant	rs755109
Chromosome Location	chr9:100696203-100696204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100684548..100686454-chr9:100694702..100696797,2	MCF-7	breast:
2	chr9:100678422..100708679-chr9:100734559..100755577,174	K562	blood:
3	chr9:100696013..100699012-chr9:100772945..100774984,2	K562	blood:
4	chr9:100695365..100698357-chr9:100723425..100724999,2	K562	blood:
5	chr9:100675954..100709047-chr9:100737887..100755543,175	K562	blood:

Variant related genes	Relation type
ENSG00000136938	Chromatin interaction
ENSG00000236896	Chromatin interaction
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10760021	0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10760022	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10984297	0.80[ASN][1000 genomes]
rs10984349	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs10984361	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10984373	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10984405	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10984462	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10984466	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10984478	0.91[ASN][1000 genomes]
rs10984484	0.91[ASN][1000 genomes]
rs10984499	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10984506	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10984588	0.84[ASN][1000 genomes]
rs10984599	0.80[ASN][1000 genomes]
rs1127703	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12235434	0.84[ASN][1000 genomes]
rs12236440	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12237296	0.82[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs12377604	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475695	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1475696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17431614	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17431934	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417577	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3183927	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3183928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3758253	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3758254	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3780416	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs3780417	0.84[ASN][1000 genomes]
rs3780418	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs3780419	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs3780420	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3808894	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3824496	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4618817	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4631576	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4743145	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4743147	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55737216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66990486	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67975003	0.96[ASN][1000 genomes]
rs68053069	0.85[ASN][1000 genomes]
rs7025609	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7030887	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7030907	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72753572	0.96[ASN][1000 genomes]
rs72753587	0.85[ASN][1000 genomes]
rs7861658	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[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	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Quantitative traits	19197348	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs755109	C9orf156	cis	cerebellum	SCAN
rs755109	TMOD1	cis	parietal	SCAN
rs755109	WNK2	cis	parietal	SCAN
rs755109	NANS	cis	cerebellum	SCAN
rs755109	HEMGN	cis	multi-tissue	Pritchard
rs755109	C9orf156	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100693400-100700400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr9:100693800-100696800	Enhancers	Primary hematopoietic stem cells	blood
3	chr9:100693800-100696800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr9:100694400-100697600	Weak transcription	Dnd41	blood
5	chr9:100694400-100699200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:100694600-100697000	Weak transcription	Thymus	Thymus
7	chr9:100694600-100700000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:100695200-100699600	Transcr. at gene 5' and 3'	K562	blood
9	chr9:100695400-100699000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr9:100695600-100700000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr9:100695800-100696400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr9:100695800-100698800	Enhancers	Fetal Thymus	thymus
13	chr9:100696000-100696400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:100696000-100696600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr9:100696000-100697800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr9:100696000-100700000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr9:100696200-100696600	Weak transcription	Primary T cells from cord blood	blood
18	chr9:100696200-100696600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:100696200-100697000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:100696200-100697000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:100696200-100697400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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