Variant report

Variant	rs12195904
Chromosome Location	chr6:109815963-109815964
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109803960..109806635-chr6:109814001..109815992,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112365	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10457192	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10457194	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10457195	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10782163	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11153183	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11153188	0.85[EUR][1000 genomes]
rs11752791	0.83[EUR][1000 genomes]
rs11754340	0.81[EUR][1000 genomes]
rs11754455	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11755641	0.82[EUR][1000 genomes]
rs12193719	0.82[EUR][1000 genomes]
rs12194061	0.85[EUR][1000 genomes]
rs12197180	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12198938	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12199154	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12212476	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12214639	0.83[EUR][1000 genomes]
rs13191066	0.81[EUR][1000 genomes]
rs13199135	0.82[EUR][1000 genomes]
rs13201947	0.81[EUR][1000 genomes]
rs13201951	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13203587	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13220915	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1406899	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1476388	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1960325	0.82[EUR][1000 genomes]
rs1998811	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2024849	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2024850	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2024852	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2024853	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2277114	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2357124	0.84[EUR][1000 genomes]
rs4490694	0.83[EUR][1000 genomes]
rs4945833	0.83[EUR][1000 genomes]
rs6906216	0.82[ASN][1000 genomes]
rs6926096	0.82[ASN][1000 genomes]
rs749517	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7755941	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7773950	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12195904	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12195904	AK9	cis	Nerve Tibial	GTEx
rs12195904	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs12195904	SMPD2	cis	Whole Blood	GTEx
rs12195904	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs12195904	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109805000-109817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:109812000-109816800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr6:109812800-109816800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:109812800-109819000	Weak transcription	Fetal Kidney	kidney
5	chr6:109813200-109816000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:109813400-109816800	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:109813400-109817000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:109813400-109817000	Weak transcription	Primary T cells from cord blood	blood
9	chr6:109813400-109817400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:109813400-109817400	Weak transcription	Placenta	Placenta
11	chr6:109813400-109817400	Weak transcription	HSMMtube	muscle
12	chr6:109813400-109818000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:109813400-109821200	Weak transcription	Thymus	Thymus
14	chr6:109813400-109823000	Weak transcription	HSMM	muscle
15	chr6:109813600-109817400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:109814600-109816400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:109814600-109816600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:109814600-109817800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:109814800-109816400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr6:109815400-109816200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr6:109815800-109817600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:109815800-109837200	Weak transcription	Primary B cells from cord blood	blood

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