Variant report

Variant	rs4847399
Chromosome Location	chr1:93584606-93584607
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	chr1:93582432..93585067-chr1:93594347..93596208,2	K562	blood:

Variant related genes	Relation type
ENSG00000143033	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1010476	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs1057257	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1060622	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10782955	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10874759	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10874762	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10874764	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1088318	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11164870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164871	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11164876	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164879	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11164881	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12030549	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12030843	0.86[CHB][hapmap]
rs12038699	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12044557	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap]
rs12044657	0.83[EUR][1000 genomes]
rs12118230	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12118262	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12124011	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12128131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130734	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12139009	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12385720	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1335679	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1474927	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1572343	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1856027	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1932314	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2152358	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2208044	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255722	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2281524	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2281525	0.82[CHB][hapmap]
rs2295423	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295424	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2297707	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2484486	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs2749732	0.87[CHD][hapmap]
rs2765545	0.91[CEU][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2783489	0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.81[ASN][1000 genomes]
rs2783490	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2783495	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2783499	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap]
rs2783500	0.85[CHB][hapmap]
rs2783501	0.86[CHB][hapmap]
rs2815429	0.88[CHD][hapmap]
rs35940311	0.86[AMR][1000 genomes]
rs3754184	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3754186	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3904666	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs4000699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4240966	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs4484937	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap]
rs4847235	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4847398	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4847401	0.81[EUR][1000 genomes]
rs4847402	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs531358	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs531514	0.83[AMR][1000 genomes]
rs547866	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs555161	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs565919	0.88[AMR][1000 genomes]
rs612037	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs622608	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs624131	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs627779	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs637646	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6541401	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6541404	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap]
rs661126	0.81[AMR][1000 genomes]
rs6682670	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6688230	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs687394	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs693737	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs7513705	0.91[CEU][hapmap];0.95[CHB][hapmap];0.80[EUR][1000 genomes]
rs7517363	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7532195	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7532549	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535628	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7539307	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs7541687	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7553465	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7553916	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs797661	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs797668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs797672	0.83[AMR][1000 genomes]
rs797675	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs797676	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs797680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][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	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
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs4847399	RP4-717I23.3	cis	Artery Tibial	GTEx
rs4847399	DR1	cis	parietal	SCAN
rs4847399	CCDC18	cis	parietal	SCAN
rs4847399	RP4-717I23.3	cis	lung	GTEx
rs4847399	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs4847399	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4847399	F3	cis	cerebellum	SCAN
rs4847399	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs4847399	RP4-717I23.3	cis	Artery Aorta	GTEx
rs4847399	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs4847399	GCLM	cis	cerebellum	SCAN
rs4847399	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs4847399	TMED5	cis	cerebellum	SCAN
rs4847399	TMED5	cis	parietal	SCAN
rs4847399	RP4-717I23.3	cis	Thyroid	GTEx
rs4847399	DR1	cis	multi-tissue	Pritchard
rs4847399	RP4-717I23.3	cis	Whole Blood	GTEx
rs4847399	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs4847399	BARHL2	cis	parietal	SCAN
rs4847399	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs4847399	RP4-717I23.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
2	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
3	chr1:93548000-93601800	Weak transcription	NHLF	lung
4	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
5	chr1:93571400-93602200	Weak transcription	Colonic Mucosa	Colon
6	chr1:93572400-93599600	Weak transcription	Spleen	Spleen
7	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:93573600-93586000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:93573800-93609000	Strong transcription	Fetal Thymus	thymus
10	chr1:93574200-93609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:93574600-93584800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:93574600-93585800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:93574600-93609000	Strong transcription	Dnd41	blood
14	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
15	chr1:93575200-93589800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:93575800-93589200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:93577200-93592800	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:93577200-93597000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:93577600-93585200	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:93577600-93586600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:93577600-93586800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:93577600-93588800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:93577600-93591400	Weak transcription	Fetal Heart	heart
24	chr1:93577800-93601600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:93578200-93587200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:93578200-93588200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:93578400-93587400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:93578400-93587600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:93578600-93586600	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:93578600-93586800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:93578600-93586800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:93578800-93613600	Weak transcription	Psoas Muscle	Psoas
33	chr1:93578800-93620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:93579600-93586800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:93579600-93587200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr1:93579600-93595400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:93579800-93586600	Strong transcription	Liver	Liver
38	chr1:93579800-93587200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:93579800-93588000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:93580000-93585800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr1:93580000-93586400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:93580000-93587600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:93580000-93587600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:93580000-93588200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:93580000-93624000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:93580200-93586600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:93580400-93585600	Strong transcription	Fetal Lung	lung
49	chr1:93580400-93585800	Strong transcription	Primary T cells from cord blood	blood
50	chr1:93580400-93586400	Strong transcription	Duodenum Mucosa	Duodenum

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