Variant report

Variant	rs35990903
Chromosome Location	chr12:9872549-9872550
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	chr12:9870894..9872831-chr12:9873111..9875756,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184293	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10161013	1.00[EUR][1000 genomes]
rs10492164	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10743828	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10772093	1.00[EUR][1000 genomes]
rs10772099	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10844656	0.94[EUR][1000 genomes]
rs11052306	0.80[EUR][1000 genomes]
rs1134543	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11835594	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304982	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12820281	0.97[EUR][1000 genomes]
rs12824727	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377908	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377939	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16923367	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16927874	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080210	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2268145	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401387	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2401388	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3136576	0.80[EUR][1000 genomes]
rs34584384	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34633868	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922289	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611290	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4763296	0.82[EUR][1000 genomes]
rs4763864	0.84[EUR][1000 genomes]
rs55715780	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56980650	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59016059	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59210706	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6488110	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6488120	0.84[EUR][1000 genomes]
rs6488121	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6488123	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6488176	0.91[EUR][1000 genomes]
rs71447599	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71447600	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301386	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74062704	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74062708	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74065337	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74065339	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74065340	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7962964	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964917	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967436	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7969022	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7976474	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2757490	chr12:9855958-9888553	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv442255	chr12:9862078-9874924	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3693109	chr12:9863968-9876091	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv976571	chr12:9868953-9873977	Enhancers Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3406286	chr12:9871143-9872940	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs35990903	RP11-75L1.2	cis	lung	GTEx
rs35990903	RP11-75L1.2	cis	Adipose Subcutaneous	GTEx
rs35990903	RP11-75L1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs35990903	RP11-75L1.2	cis	Nerve Tibial	GTEx
rs35990903	RP11-75L1.2	cis	Whole Blood	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9861000-9873200	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr12:9861000-9874200	Weak transcription	Fetal Thymus	thymus
3	chr12:9861600-9882400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:9861800-9874000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:9864000-9873600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:9864600-9883800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:9868400-9872600	Weak transcription	HUVEC	blood vessel
8	chr12:9868600-9879200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:9869200-9874200	Weak transcription	K562	blood
10	chr12:9871000-9874000	Enhancers	Primary B cells from cord blood	blood
11	chr12:9871400-9873600	Enhancers	A549	lung
12	chr12:9872200-9872800	Flanking Active TSS	GM12878-XiMat	blood
13	chr12:9872200-9873600	Genic enhancers	Primary B cells from peripheral blood	blood
14	chr12:9872400-9872600	Weak transcription	Rectal Mucosa Donor 29	rectum

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