Variant report

Variant	rs11164848
Chromosome Location	chr1:93421110-93421111
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	chr1:93418758..93421387-chr1:93428230..93431121,2	MCF-7	breast:
2	chr1:93420417..93422302-chr1:93426239..93427942,2	K562	blood:

Variant related genes	Relation type
ENSG00000154511	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10874752	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164838	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164849	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12092304	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747275	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847386	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847389	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs514235	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs521428	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs606344	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs619784	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs641462	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs660870	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6671078	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6671268	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6681240	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681345	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs753391	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs770884	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11164848	FAM69A	cis	Artery Tibial	GTEx
rs11164848	MTF2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93400800-93421800	Weak transcription	Fetal Lung	lung
2	chr1:93409200-93421200	Weak transcription	Fetal Brain Female	brain
3	chr1:93409600-93426000	Weak transcription	Lung	lung
4	chr1:93410600-93425600	Weak transcription	Aorta	Aorta
5	chr1:93410600-93425800	Weak transcription	Right Atrium	heart
6	chr1:93410600-93426000	Weak transcription	Left Ventricle	heart
7	chr1:93411000-93422000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:93411000-93425800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:93412400-93422000	Weak transcription	Liver	Liver
10	chr1:93413600-93425600	Enhancers	Primary B cells from peripheral blood	blood
11	chr1:93415200-93425600	Enhancers	Primary T cells from cord blood	blood
12	chr1:93415200-93425600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:93415200-93425600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:93415200-93425600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr1:93415600-93422800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:93416400-93422200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:93416400-93422600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:93417000-93425400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:93417000-93425600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:93417000-93425600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:93417000-93425800	Weak transcription	Right Ventricle	heart
22	chr1:93417200-93421800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:93417200-93421800	Weak transcription	Fetal Intestine Small	intestine
24	chr1:93417200-93422000	Weak transcription	Adipose Nuclei	Adipose
25	chr1:93417200-93422000	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:93417200-93422200	Weak transcription	Fetal Intestine Large	intestine
27	chr1:93417200-93423800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:93417200-93425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:93417400-93421800	Weak transcription	Stomach Mucosa	stomach
30	chr1:93417400-93422200	Weak transcription	HSMMtube	muscle
31	chr1:93417400-93422400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:93417400-93423200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:93417600-93422000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:93417600-93422800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:93417600-93425600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:93417600-93425600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:93417800-93421600	Weak transcription	K562	blood
38	chr1:93417800-93421800	Weak transcription	Brain Angular Gyrus	brain
39	chr1:93417800-93422200	Weak transcription	Thymus	Thymus
40	chr1:93417800-93422600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:93417800-93423000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:93417800-93425600	Weak transcription	NHLF	lung
43	chr1:93418000-93425600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:93418200-93421200	Weak transcription	Fetal Thymus	thymus
45	chr1:93418200-93421800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:93418200-93425800	Weak transcription	Psoas Muscle	Psoas
47	chr1:93418600-93422000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:93418600-93422000	Weak transcription	A549	lung
49	chr1:93419000-93421800	Weak transcription	Small Intestine	intestine
50	chr1:93419200-93421800	Weak transcription	HepG2	liver

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