Variant report

Variant	rs6912084
Chromosome Location	chr6:14872046-14872047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:14862977..14865846-chr6:14871194..14873734,2	MCF-7	breast:
2	chr6:14870064..14872343-chr6:14875249..14877493,2	K562	blood:
3	chr6:14870368..14872279-chr6:14881525..14883346,2	K562	blood:
4	chr6:14870064..14873401-chr6:14874524..14877493,5	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10949261	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374664	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258993	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16875778	0.80[AMR][1000 genomes]
rs16875782	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16875788	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16875810	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124291	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2168315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373633	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs387877	0.93[EUR][1000 genomes]
rs389438	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs394849	0.94[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs403392	0.94[EUR][1000 genomes]
rs410494	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41472949	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs423468	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs425233	0.94[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs443427	0.94[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs52875	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs62390307	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62390308	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390309	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62390310	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390312	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62390313	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390314	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62390316	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390318	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390319	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390320	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390321	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6912613	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826859	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826868	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826874	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72826878	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9476670	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9476671	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9476672	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv1031668	chr6:14774036-15044308	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538138	chr6:14774036-15044308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1017572	chr6:14830510-14906933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6912084	TBC1D7	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:14864800-14874600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:14864800-14880600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:14865000-14874400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:14866200-14875400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:14866400-14873000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:14866400-14873000	Weak transcription	Primary T cells from cord blood	blood
7	chr6:14866600-14872800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:14866600-14874400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:14866600-14874400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:14866600-14874600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:14866600-14880400	Weak transcription	Spleen	Spleen
12	chr6:14867000-14876600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:14867400-14873400	Weak transcription	Primary B cells from cord blood	blood
14	chr6:14869400-14875400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:14869600-14875200	Enhancers	Fetal Thymus	thymus
16	chr6:14870800-14872400	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr6:14870800-14872400	Weak transcription	Thymus	Thymus
18	chr6:14870800-14874200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:14870800-14874600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:14871000-14872400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:14871000-14873000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:14871400-14872400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:14871400-14872400	Enhancers	Fetal Lung	lung
24	chr6:14871400-14873000	Enhancers	Left Ventricle	heart
25	chr6:14871600-14872800	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr6:14871600-14877000	Weak transcription	HSMM	muscle
27	chr6:14871600-14886600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr6:14871800-14872200	Weak transcription	Psoas Muscle	Psoas
29	chr6:14872000-14875000	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr6:14872000-14877200	Weak transcription	Fetal Heart	heart
31	chr6:14872000-14877200	Weak transcription	HSMMtube	muscle

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