Variant report

Variant	rs41472949
Chromosome Location	chr6:14864577-14864578
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	chr6:14864567..14867546-chr6:15247170..15248965,2	K562	blood:
3	chr6:14856336..14859262-chr6:14863134..14864951,2	K562	blood:

Variant related genes	Relation type
ENSG00000235488	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12190539	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs1258993	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs16875788	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2168315	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs373633	0.94[CEU][hapmap]
rs389438	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs394849	0.87[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs423468	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs425233	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs443427	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs52875	0.94[CEU][hapmap];0.90[JPT][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	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
rs41472949	TBC1D7	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:14850400-14866200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:14858400-14864600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:14858400-14865600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr6:14858400-14865800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:14858400-14866000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:14860000-14865800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:14862000-14864600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:14862000-14865400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:14862000-14865800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:14862000-14865800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:14862000-14865800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:14862000-14865800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:14862200-14864600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:14862200-14864800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:14862200-14865800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:14862200-14865800	Weak transcription	Fetal Thymus	thymus
17	chr6:14863200-14865400	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr6:14863400-14866200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr6:14863600-14868400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr6:14863800-14866400	Enhancers	K562	blood
21	chr6:14864000-14864600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr6:14864000-14865000	Enhancers	H1 Cell Line	embryonic stem cell
23	chr6:14864000-14865000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:14864200-14864600	Enhancers	Brain Anterior Caudate	brain
25	chr6:14864200-14864600	Enhancers	Spleen	Spleen
26	chr6:14864200-14864800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr6:14864200-14864800	Enhancers	Primary B cells from peripheral blood	blood
28	chr6:14864200-14864800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr6:14864200-14864800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr6:14864200-14865000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr6:14864200-14865200	Enhancers	Fetal Muscle Leg	muscle
32	chr6:14864200-14866000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:14864200-14866400	Enhancers	Colon Smooth Muscle	Colon
34	chr6:14864200-14866600	Enhancers	Fetal Kidney	kidney
35	chr6:14864200-14867400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:14864400-14864800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:14864400-14864800	Enhancers	H9 Cell Line	embryonic stem cell
38	chr6:14864400-14864800	Enhancers	Fetal Intestine Small	intestine
39	chr6:14864400-14864800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr6:14864400-14865000	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr6:14864400-14865000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:14864400-14865000	Enhancers	Ovary	ovary
43	chr6:14864400-14865200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr6:14864400-14866400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:14864400-14866400	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr6:14864400-14866600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:14864400-14866600	Enhancers	Fetal Stomach	stomach

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