Variant report

Variant	rs4638383
Chromosome Location	chr12:121190302-121190303
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121186636..121188144-chr12:121188175..121190452,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1027556	1.00[YRI][hapmap]
rs1039302	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs10431387	1.00[ASW][hapmap];0.80[GIH][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs10437838	1.00[ASW][hapmap];0.82[GIH][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10744754	0.83[AMR][1000 genomes]
rs10774568	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs10774569	1.00[YRI][hapmap]
rs10774571	1.00[YRI][hapmap]
rs10849782	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10849786	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs10849787	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10849788	1.00[ASW][hapmap];0.82[GIH][hapmap];0.95[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10849790	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10849810	1.00[YRI][hapmap]
rs10849811	1.00[YRI][hapmap]
rs11065259	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11065298	1.00[YRI][hapmap]
rs11065322	1.00[ASW][hapmap];0.80[GIH][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs1151849	0.86[YRI][hapmap]
rs1151862	0.86[YRI][hapmap]
rs11829904	0.81[YRI][hapmap]
rs11833706	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13746	0.83[YRI][hapmap]
rs2393718	1.00[YRI][hapmap]
rs2393725	0.95[AFR][1000 genomes]
rs3213568	1.00[ASW][hapmap];0.82[GIH][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3213571	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3809314	1.00[ASW][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs471688	0.86[YRI][hapmap]
rs508595	0.80[YRI][hapmap]
rs531782	0.93[YRI][hapmap]
rs610694	0.86[YRI][hapmap]
rs624216	0.86[YRI][hapmap]
rs625228	0.83[LWK][hapmap];0.93[YRI][hapmap]
rs6489780	1.00[ASW][hapmap];0.82[GIH][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6489782	1.00[ASW][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap]
rs7135147	1.00[ASW][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs7135426	0.84[AFR][1000 genomes]
rs7139145	1.00[YRI][hapmap]
rs715319	1.00[ASW][hapmap];0.80[GIH][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs7298639	1.00[YRI][hapmap]
rs7300695	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs73229114	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7960784	0.83[AFR][1000 genomes]
rs7965332	1.00[YRI][hapmap]
rs7977343	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1041153	chr12:121171986-121208826	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4638383	RNFT2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121168600-121196400	Weak transcription	Fetal Brain Female	brain
2	chr12:121177800-121197800	Weak transcription	Gastric	stomach
3	chr12:121178000-121194400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:121179800-121197400	Weak transcription	Spleen	Spleen
5	chr12:121180200-121197400	Weak transcription	Pancreas	Pancrea
6	chr12:121183200-121197600	Weak transcription	Esophagus	oesophagus
7	chr12:121186400-121198400	Weak transcription	Right Ventricle	heart
8	chr12:121186600-121192400	Weak transcription	Fetal Intestine Small	intestine
9	chr12:121189600-121197000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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