Variant report

Variant	rs12193312
Chromosome Location	chr6:53605294-53605295
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	chr6:53598898..53601641-chr6:53603723..53606379,2	MCF-7	breast:
2	chr6:53603213..53606013-chr6:53606213..53607991,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10456164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10456671	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12197259	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13191282	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13195168	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13196802	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13206978	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13211007	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13219456	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3000995	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3003502	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4302662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4409173	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4416674	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4428502	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4443499	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4469293	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4479931	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4555913	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4574642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4715423	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458955	0.85[EUR][1000 genomes]
rs6909833	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930030	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930035	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7745277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7755196	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7755522	0.97[AMR][1000 genomes];0.91[EUR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12193312	LRRC1	Cis_1M	lymphoblastoid	RTeQTL
rs12193312	KLHL31	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53596000-53605600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:53599800-53606200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:53600000-53605800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:53600800-53606200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr6:53601000-53606000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr6:53601000-53606200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:53601200-53605800	Weak transcription	Primary T cells from cord blood	blood
8	chr6:53601200-53605800	Weak transcription	Thymus	Thymus
9	chr6:53601200-53606000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:53601200-53606000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:53601200-53606000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:53601200-53606000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:53601200-53606200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:53601800-53613400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:53602200-53606400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:53602200-53614800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:53602800-53605800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:53603000-53608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:53603000-53608800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:53603200-53608000	Weak transcription	NHEK	skin
22	chr6:53603200-53609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:53603400-53605600	Weak transcription	HepG2	liver
24	chr6:53603400-53605800	Weak transcription	Fetal Thymus	thymus
25	chr6:53603600-53607800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:53603600-53608000	Weak transcription	Placenta	Placenta
27	chr6:53604600-53605800	Enhancers	Dnd41	blood
28	chr6:53605200-53605400	Enhancers	Fetal Intestine Small	intestine
29	chr6:53605200-53606600	Enhancers	Fetal Intestine Large	intestine

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