Variant report

Variant	rs4847386
Chromosome Location	chr1:93420907-93420908
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	chr1:93418758..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: 29 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1011663	0.81[JPT][hapmap]
rs10874752	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]
rs11164827	0.84[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs11164838	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164848	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164849	0.86[AMR][1000 genomes];0.99[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747275	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3943283	0.81[JPT][hapmap]
rs4847389	0.83[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs514235	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs521428	0.83[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs567613	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs606344	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs619784	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs641462	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs660870	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6671078	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6671268	0.94[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[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	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7524934	0.81[JPT][hapmap]
rs753391	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs770883	0.81[JPT][hapmap]
rs770884	0.92[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4847386	FAM69A	cis	Artery Tibial	GTEx
rs4847386	BARHL2	cis	parietal	SCAN
rs4847386	MTF2	cis	Skin Sun Exposed Lower leg	GTEx
rs4847386	CDC73	trans	cerebellum	SCAN

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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