Variant report

Variant	rs12190539
Chromosome Location	chr6:14865266-14865267
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:14862977..14865846-chr6:14871194..14873734,2	MCF-7	breast:
2	chr6:14864567..14867546-chr6:15247170..15248965,2	K562	blood:

Variant related genes	Relation type
ENSG00000235488	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10949261	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12374664	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258993	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16875788	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16875810	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124291	0.82[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];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373633	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs387877	0.99[EUR][1000 genomes]
rs389438	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs394849	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs403392	0.97[EUR][1000 genomes]
rs410494	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41472949	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs423468	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs425233	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs443427	0.94[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs52875	0.87[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes]
rs62390307	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62390308	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390309	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62390310	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390312	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62390313	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390314	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62390316	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390318	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390319	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390320	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62390321	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6912084	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912613	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826859	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826868	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826874	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72826878	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9476670	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9476671	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9476672	0.85[AMR][1000 genomes];0.96[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

No data

Chromatin state (count:44 , 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	chr6:14858400-14865600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr6:14858400-14865800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:14858400-14866000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:14860000-14865800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr6:14862000-14865400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:14862000-14865800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:14862000-14865800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:14862000-14865800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:14862000-14865800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:14862200-14865800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:14862200-14865800	Weak transcription	Fetal Thymus	thymus
13	chr6:14863200-14865400	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr6:14863400-14866200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:14863600-14868400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:14863800-14866400	Enhancers	K562	blood
17	chr6:14864200-14866000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:14864200-14866400	Enhancers	Colon Smooth Muscle	Colon
19	chr6:14864200-14866600	Enhancers	Fetal Kidney	kidney
20	chr6:14864200-14867400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:14864400-14866400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:14864400-14866400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr6:14864400-14866600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:14864400-14866600	Enhancers	Fetal Stomach	stomach
25	chr6:14864600-14865800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:14864600-14865800	Weak transcription	Right Atrium	heart
27	chr6:14864600-14866200	Weak transcription	Spleen	Spleen
28	chr6:14864600-14867400	Enhancers	Primary B cells from cord blood	blood
29	chr6:14864800-14865400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr6:14864800-14865400	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr6:14864800-14865800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:14864800-14865800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:14864800-14866200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:14864800-14874600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:14864800-14880600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:14865000-14865800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:14865000-14866000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:14865000-14866000	Weak transcription	Adipose Nuclei	Adipose
39	chr6:14865000-14866000	Weak transcription	Ovary	ovary
40	chr6:14865000-14870200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr6:14865000-14874400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr6:14865200-14865600	Weak transcription	Fetal Muscle Leg	muscle
43	chr6:14865200-14866000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr6:14865200-14866200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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