Variant report

Variant	rs12526662
Chromosome Location	chr6:44079216-44079217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44069212..44071574-chr6:44077643..44079819,2	MCF-7	breast:
2	chr6:44076515..44082841-chr6:44082960..44087705,9	MCF-7	breast:
3	chr6:44078325..44080671-chr6:44098059..44099974,2	MCF-7	breast:
4	chr6:44064707..44066979-chr6:44078095..44080647,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10428726	0.96[ASN][1000 genomes]
rs10807295	0.96[ASN][1000 genomes]
rs10948122	1.00[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948123	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948125	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10948126	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11966587	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967633	0.96[ASN][1000 genomes]
rs11968386	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525049	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12664793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096200	0.96[ASN][1000 genomes]
rs3188	1.00[JPT][hapmap]
rs35738079	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs41282654	0.93[ASN][1000 genomes]
rs4711765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714749	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55862642	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59028814	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60245793	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60691447	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912142	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs700006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713050	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73733834	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7738970	0.96[ASN][1000 genomes]
rs7771710	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877112	0.93[MKK][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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv462935	chr6:44046143-44117607	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv603002	chr6:44046143-44117607	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12526662	FRS3	cis	cerebellum	SCAN
rs12526662	MRPL14	cis	cerebellum	SCAN
rs12526662	GPR110	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44058800-44093600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:44066000-44081400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:44066000-44091000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:44066400-44082200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:44066800-44079400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:44067000-44084200	Strong transcription	Brain Germinal Matrix	brain
7	chr6:44067000-44084400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:44067200-44085000	Strong transcription	Dnd41	blood
9	chr6:44067600-44079600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:44070000-44083200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:44070400-44084000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:44070600-44084000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:44070800-44079600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:44070800-44084200	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:44071000-44081600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:44071000-44084600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:44071200-44080000	Strong transcription	Gastric	stomach
18	chr6:44071200-44083400	Strong transcription	Fetal Thymus	thymus
19	chr6:44071200-44084200	Strong transcription	Fetal Brain Female	brain
20	chr6:44071200-44084600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:44071200-44084600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:44071200-44086400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:44071400-44082200	Strong transcription	Primary B cells from cord blood	blood
24	chr6:44071400-44083800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:44071400-44083800	Strong transcription	Primary T cells from cord blood	blood
26	chr6:44071400-44084400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:44071400-44084400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr6:44071600-44081800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:44071600-44083200	Strong transcription	K562	blood
30	chr6:44071600-44084000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:44071600-44084200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr6:44071600-44084400	Strong transcription	GM12878-XiMat	blood
33	chr6:44071800-44083600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr6:44071800-44084000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr6:44071800-44084400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:44072400-44081400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:44073000-44081000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:44073200-44084400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:44073800-44082400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:44073800-44083800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr6:44073800-44084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:44074000-44086600	Strong transcription	Fetal Stomach	stomach
43	chr6:44074400-44083200	Strong transcription	Osteobl	bone
44	chr6:44074400-44083600	Strong transcription	NHLF	lung
45	chr6:44074600-44083200	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr6:44074600-44084200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr6:44074600-44084200	Strong transcription	Hela-S3	cervix
48	chr6:44074800-44083400	Strong transcription	Adipose Nuclei	Adipose
49	chr6:44074800-44083400	Strong transcription	Thymus	Thymus
50	chr6:44074800-44084200	Strong transcription	H9 Cell Line	embryonic stem cell

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