Variant report

Variant	rs6770670
Chromosome Location	chr3:49686682-49686683
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49576104..49578514-chr3:49684857..49687792,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1050088	0.86[JPT][hapmap]
rs1060962	0.81[ASN][1000 genomes]
rs10865955	0.86[JPT][hapmap]
rs11130199	0.86[JPT][hapmap]
rs11130212	0.97[ASN][1000 genomes]
rs11130213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1131095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11709525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710037	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711485	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs11718165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720264	0.88[JPT][hapmap]
rs11720597	0.85[AMR][1000 genomes]
rs11917431	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919311	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11921590	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489092	0.88[JPT][hapmap]
rs13064576	0.85[AMR][1000 genomes]
rs13085791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13316695	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352890	0.92[ASN][1000 genomes]
rs1568661	0.86[JPT][hapmap]
rs1801143	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs1873625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1873626	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2005557	0.81[ASN][1000 genomes]
rs2131104	0.81[ASN][1000 genomes]
rs2172252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329020	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2960548	0.87[ASN][1000 genomes]
rs3197999	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34762726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007338	0.92[ASN][1000 genomes]
rs35404120	0.92[ASN][1000 genomes]
rs35701831	0.86[JPT][hapmap]
rs3811697	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs3870338	0.86[JPT][hapmap]
rs3924462	0.86[JPT][hapmap]
rs4283605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs4855839	0.86[JPT][hapmap]
rs4855847	0.92[ASN][1000 genomes]
rs4855852	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855859	0.86[JPT][hapmap]
rs4855864	0.86[JPT][hapmap]
rs4855881	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855884	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6765869	0.81[ASN][1000 genomes]
rs6766131	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs6803222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7614725	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622302	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs7633271	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs7637999	0.86[JPT][hapmap]
rs885592	0.86[JPT][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9812791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822268	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9824092	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827021	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs9827708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833611	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9836291	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9837027	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9837341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837520	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9841110	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs9853683	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9858213	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs9858280	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9858542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862080	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875617	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs9882740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6770670	FAM212A	cis	Muscle Skeletal	GTEx
rs6770670	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs6770670	IHPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49661600-49692400	Weak transcription	Ovary	ovary
2	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:49673800-49692400	Weak transcription	Gastric	stomach
4	chr3:49675400-49688200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:49676200-49692000	Weak transcription	Esophagus	oesophagus
6	chr3:49676400-49687000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:49679600-49687000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:49679800-49687600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr3:49681200-49688600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49681200-49688800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:49682200-49689000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:49682600-49688400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:49683000-49687000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:49684600-49687400	Enhancers	Fetal Heart	heart
15	chr3:49684600-49687800	Genic enhancers	Brain Inferior Temporal Lobe	brain
16	chr3:49684800-49687400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:49684800-49687400	Enhancers	Left Ventricle	heart
18	chr3:49684800-49687600	Enhancers	Psoas Muscle	Psoas
19	chr3:49684800-49688000	Enhancers	HepG2	liver
20	chr3:49684800-49688400	Enhancers	Fetal Muscle Leg	muscle
21	chr3:49684800-49688800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:49684800-49689400	Enhancers	Fetal Muscle Trunk	muscle
23	chr3:49685000-49687400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:49685000-49687600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
26	chr3:49685400-49687600	Enhancers	K562	blood
27	chr3:49685400-49690400	Weak transcription	Lung	lung
28	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
29	chr3:49685600-49686800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:49685600-49687000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:49685600-49687000	Weak transcription	NH-A	brain
32	chr3:49685600-49693200	Weak transcription	Liver	Liver
33	chr3:49685800-49687000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:49685800-49687000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:49685800-49688400	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:49685800-49688400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:49685800-49689000	Weak transcription	Fetal Stomach	stomach
38	chr3:49685800-49689600	Weak transcription	Brain Substantia Nigra	brain
39	chr3:49685800-49692600	Weak transcription	Fetal Intestine Small	intestine
40	chr3:49686000-49687000	Weak transcription	GM12878-XiMat	blood
41	chr3:49686000-49687600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr3:49686000-49688400	Weak transcription	Brain Anterior Caudate	brain
43	chr3:49686000-49689000	Weak transcription	Brain Angular Gyrus	brain
44	chr3:49686000-49692400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:49686000-49692600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:49686400-49687600	Enhancers	Spleen	Spleen
47	chr3:49686400-49687800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:49686600-49687000	Weak transcription	Right Ventricle	heart
49	chr3:49686600-49688200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:49686600-49697200	Weak transcription	Pancreas	Pancrea

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