Variant report

Variant	rs10874752
Chromosome Location	chr1:93421930-93421931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93420417..93422302-chr1:93426239..93427942,2	K562	blood:
2	chr1:93421789..93424447-chr1:93426691..93429182,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154511	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1011663	0.81[JPT][hapmap]
rs11164827	0.89[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs11164838	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11164848	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164849	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164850	0.81[JPT][hapmap]
rs11164851	0.81[JPT][hapmap]
rs11164854	0.81[JPT][hapmap]
rs12092304	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747275	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3943283	0.81[JPT][hapmap]
rs4847386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847389	0.88[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs514235	0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs521428	0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs567613	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs606344	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs619784	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs641462	0.89[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs660870	0.89[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6671078	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6671268	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6681240	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681345	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7524934	0.81[JPT][hapmap]
rs753391	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs770883	0.81[JPT][hapmap]
rs770884	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10874752	FAM69A	cis	Artery Tibial	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93409600-93426000	Weak transcription	Lung	lung
2	chr1:93410600-93425600	Weak transcription	Aorta	Aorta
3	chr1:93410600-93425800	Weak transcription	Right Atrium	heart
4	chr1:93410600-93426000	Weak transcription	Left Ventricle	heart
5	chr1:93411000-93422000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:93411000-93425800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:93412400-93422000	Weak transcription	Liver	Liver
8	chr1:93413600-93425600	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:93415200-93425600	Enhancers	Primary T cells from cord blood	blood
10	chr1:93415200-93425600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:93415200-93425600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr1:93415200-93425600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:93415600-93422800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:93416400-93422200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:93416400-93422600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:93417000-93425400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:93417000-93425600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:93417000-93425600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:93417000-93425800	Weak transcription	Right Ventricle	heart
20	chr1:93417200-93422000	Weak transcription	Adipose Nuclei	Adipose
21	chr1:93417200-93422000	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:93417200-93422200	Weak transcription	Fetal Intestine Large	intestine
23	chr1:93417200-93423800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:93417200-93425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:93417400-93422200	Weak transcription	HSMMtube	muscle
26	chr1:93417400-93422400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:93417400-93423200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:93417600-93422000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:93417600-93422800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:93417600-93425600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:93417600-93425600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:93417800-93422200	Weak transcription	Thymus	Thymus
33	chr1:93417800-93422600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:93417800-93423000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:93417800-93425600	Weak transcription	NHLF	lung
36	chr1:93418000-93425600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:93418200-93425800	Weak transcription	Psoas Muscle	Psoas
38	chr1:93418600-93422000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:93418600-93422000	Weak transcription	A549	lung
40	chr1:93419200-93423000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:93419200-93423600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:93419200-93425600	Enhancers	Primary B cells from cord blood	blood
43	chr1:93419400-93422800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:93419400-93425600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:93419600-93422400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:93420000-93425600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:93420200-93422200	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr1:93420400-93423000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:93420400-93424400	Enhancers	Brain Substantia Nigra	brain
50	chr1:93420400-93424600	Enhancers	Brain Hippocampus Middle	brain

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