Variant report

Variant	rs2958154
Chromosome Location	chr12:57065713-57065714
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57037718..57040300-chr12:57063867..57067067,3	MCF-7	breast:
2	chr12:57065480..57067011-chr12:57068619..57070888,2	K562	blood:
3	chr12:57065416..57068047-chr12:57082190..57083976,3	MCF-7	breast:
4	chr12:57028931..57030772-chr12:57065141..57066726,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110955	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000207031	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1020848	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1026565	0.90[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs10450	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs10747769	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783794	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10876913	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876914	1.00[ASN][1000 genomes]
rs10876915	1.00[ASN][1000 genomes]
rs10876916	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1107479	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171916	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171917	1.00[ASN][1000 genomes]
rs11171951	0.89[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs11835120	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837319	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12229457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465081	1.00[ASN][1000 genomes]
rs1466382	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs1563896	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1563897	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1962963	0.88[ASN][1000 genomes]
rs1979325	0.93[CHB][hapmap]
rs2035081	0.90[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs2255074	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290893	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2290894	0.90[CEU][hapmap];0.93[CHB][hapmap]
rs2926740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926741	0.90[CEU][hapmap];0.93[CHB][hapmap]
rs2926743	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2950387	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[ASN][1000 genomes]
rs2950388	1.00[ASN][1000 genomes]
rs2950389	0.90[JPT][hapmap]
rs2950390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950393	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950394	1.00[ASN][1000 genomes]
rs2958123	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958124	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958127	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs2958130	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs2958145	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2958146	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958148	0.89[CEU][hapmap]
rs2958149	0.87[CHB][hapmap]
rs2958153	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs2958155	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3214051	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.84[TSI][hapmap]
rs36012661	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759028	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4759254	0.80[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs67046307	1.00[ASN][1000 genomes]
rs7295862	1.00[CEU][hapmap]
rs7297289	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7303216	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7313074	0.93[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap]
rs7315472	1.00[ASN][1000 genomes]
rs73337030	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957300	0.80[EUR][1000 genomes]
rs7967600	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap]
rs7972420	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7973157	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975783	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978685	0.93[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap]
rs7980317	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap]
rs7980378	0.94[ASN][1000 genomes]
rs7980835	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs898609	0.90[CEU][hapmap];0.93[CHB][hapmap]
rs898611	0.90[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap]
rs9368	0.81[CHB][hapmap]
rs941207	0.93[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs941209	0.84[JPT][hapmap]
rs9634246	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9634247	0.97[ASN][1000 genomes]
rs9634277	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9989034	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2958154	SPRYD3	cis	parietal	SCAN
rs2958154	PRIM1	cis	cerebellum	SCAN
rs2958154	RAB5B	cis	cerebellum	SCAN
rs2958154	PRIM1	cis	parietal	SCAN
rs2958154	LETMD1	cis	cerebellum	SCAN
rs2958154	OR10A7	cis	parietal	SCAN
rs2958154	IL23A	cis	cerebellum	SCAN
rs2958154	GPR182	cis	parietal	SCAN
rs2958154	HOXC6	cis	cerebellum	SCAN
rs2958154	HSD17B6	cis	cerebellum	SCAN
rs2958154	KRT1	cis	cerebellum	SCAN
rs2958154	CELA1	cis	cerebellum	SCAN
rs2958154	ERBB3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57040400-57069400	Weak transcription	Right Atrium	heart
2	chr12:57052400-57078200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:57054200-57069600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:57054600-57067000	Strong transcription	Muscle Satellite Cultured Cells	--
5	chr12:57054800-57075800	Strong transcription	Fetal Thymus	thymus
6	chr12:57054800-57076600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:57055400-57066400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:57055400-57066800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:57055600-57066000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:57055600-57066600	Strong transcription	Adipose Nuclei	Adipose
11	chr12:57055600-57067200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:57055600-57068200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:57055600-57077400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:57055800-57065800	Strong transcription	Primary T cells from cord blood	blood
15	chr12:57055800-57066400	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:57055800-57066600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:57055800-57067000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr12:57056000-57068000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:57056000-57069200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:57056200-57065800	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:57056200-57066200	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:57056200-57067200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:57056400-57066600	Strong transcription	Brain Germinal Matrix	brain
24	chr12:57056400-57067200	Strong transcription	Placenta	Placenta
25	chr12:57056400-57068000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:57056400-57068200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:57056400-57068200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:57056600-57066200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:57056600-57067000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:57056600-57067000	Strong transcription	NH-A	brain
31	chr12:57056600-57067200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:57056600-57067200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:57056600-57067200	Strong transcription	HUVEC	blood vessel
34	chr12:57056600-57068000	Strong transcription	GM12878-XiMat	blood
35	chr12:57056800-57065800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:57056800-57066400	Strong transcription	Brain Anterior Caudate	brain
37	chr12:57056800-57066400	Strong transcription	NHDF-Ad	bronchial
38	chr12:57056800-57066600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:57056800-57066800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:57056800-57067000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:57056800-57067200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:57056800-57067800	Strong transcription	Dnd41	blood
43	chr12:57056800-57068200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:57056800-57068200	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:57056800-57068200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:57056800-57068200	Strong transcription	HSMM	muscle
47	chr12:57057000-57067000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr12:57057400-57066800	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:57057600-57068200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr12:57057800-57066200	Strong transcription	Brain Cingulate Gyrus	brain

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