Variant report

Variant	rs425233
Chromosome Location	chr6:14879296-14879297
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:14873522..14875982-chr6:14876555..14879315,2	K562	blood:
2	chr6:14878630..14881043-chr6:14886019..14889778,3	K562	blood:
3	chr6:14861978..14864557-chr6:14877421..14879911,2	MCF-7	breast:
4	chr6:14879278..14882861-chr6:15247379..15250654,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235488	Chromatin interaction
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10949261	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12190539	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12374664	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1258993	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs16875788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16875810	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2124291	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2168315	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs373633	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs387877	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs389438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394849	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403392	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs410494	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41472949	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs423468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs52875	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62390307	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390308	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62390309	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390310	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62390312	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390313	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62390314	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390316	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62390318	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62390319	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62390320	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62390321	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912084	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6912613	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72826859	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72826868	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72826874	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826878	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9476670	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9476671	0.96[EUR][1000 genomes]
rs9476672	0.94[EUR][1000 genomes];0.82[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
rs425233	TBC1D7	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:14864800-14880600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:14866600-14880400	Weak transcription	Spleen	Spleen
3	chr6:14871600-14886600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:14875000-14882600	Weak transcription	Fetal Intestine Small	intestine
5	chr6:14875600-14880200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:14875600-14882600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:14876600-14882000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:14876800-14883600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:14877400-14880400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:14877400-14882800	Weak transcription	Lung	lung
11	chr6:14877400-14889000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:14877600-14880200	Weak transcription	Brain Anterior Caudate	brain
13	chr6:14877600-14880400	Weak transcription	Fetal Stomach	stomach
14	chr6:14877600-14880800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:14877600-14882600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:14877600-14882600	Weak transcription	Hela-S3	cervix
17	chr6:14877800-14880200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:14877800-14881000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:14877800-14881200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:14877800-14881200	Weak transcription	NHDF-Ad	bronchial
21	chr6:14877800-14881200	Weak transcription	NHLF	lung
22	chr6:14877800-14881400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:14877800-14881400	Weak transcription	Stomach Mucosa	stomach
24	chr6:14877800-14883000	Weak transcription	Fetal Kidney	kidney
25	chr6:14878000-14880000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:14878000-14880400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:14878000-14881200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:14878000-14881400	Weak transcription	HMEC	breast
29	chr6:14878200-14879600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr6:14878200-14879800	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:14878200-14880200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:14878200-14880200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr6:14878200-14881400	Weak transcription	Osteobl	bone
34	chr6:14878200-14882600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:14878200-14882600	Weak transcription	Fetal Heart	heart
36	chr6:14878200-14885600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:14878400-14879800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:14878400-14880200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr6:14878400-14880200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:14878400-14880200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:14878400-14880200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:14878400-14880200	Weak transcription	Adipose Nuclei	Adipose
43	chr6:14878400-14880200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:14878400-14880200	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:14878400-14880200	Weak transcription	Right Atrium	heart
46	chr6:14878400-14880400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:14878400-14880400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:14878400-14880400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr6:14878400-14880400	Weak transcription	Psoas Muscle	Psoas
50	chr6:14878400-14880400	Weak transcription	Small Intestine	intestine

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