Variant report

Variant	rs6554348
Chromosome Location	chr4:57219592-57219593
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	chr4:57215250..57218405-chr4:57219428..57221610,3	K562	blood:
2	chr4:57218340..57220899-chr4:57253048..57255780,3	K562	blood:

Variant related genes	Relation type
ENSG00000157426	Chromatin interaction
ENSG00000269921	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10031012	0.93[ASN][1000 genomes]
rs10031550	0.82[EUR][1000 genomes]
rs11133438	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11133439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610	0.95[JPT][hapmap]
rs11724302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11733474	1.00[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs12646703	1.00[JPT][hapmap]
rs13114104	0.90[CEU][hapmap]
rs13133016	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13138648	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13141793	0.81[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13147824	0.87[CEU][hapmap]
rs13147900	0.81[CEU][hapmap]
rs1356787	0.95[JPT][hapmap]
rs1401904	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs1401912	0.87[CEU][hapmap];0.84[YRI][hapmap]
rs2030362	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2139512	0.87[CEU][hapmap]
rs2292985	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2899063	0.87[CEU][hapmap];0.90[TSI][hapmap]
rs4167	0.87[CEU][hapmap];0.90[TSI][hapmap]
rs4864578	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4864581	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4865090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554345	0.88[CEU][hapmap]
rs6554349	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554355	0.87[CEU][hapmap];0.88[YRI][hapmap]
rs6554356	0.87[CEU][hapmap];0.86[YRI][hapmap]
rs6584	0.95[JPT][hapmap]
rs6816268	0.95[JPT][hapmap]
rs6826795	0.83[CEU][hapmap];0.90[TSI][hapmap]
rs6830518	0.95[JPT][hapmap]
rs6834736	0.82[ASW][hapmap];0.88[CEU][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.88[YRI][hapmap]
rs6836864	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6848187	0.95[JPT][hapmap]
rs6856845	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7683781	0.87[CEU][hapmap];0.90[TSI][hapmap]
rs7689163	0.91[JPT][hapmap]
rs7692385	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7693137	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693683	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9312673	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9683679	0.87[CEU][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap]
rs9684298	0.87[CEU][hapmap];0.88[TSI][hapmap];0.80[YRI][hapmap]
rs9762333	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6554348	AASDH	cis	cerebellum	SCAN
rs6554348	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs6554348	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs6554348	AASDH	cis	multi-tissue	Pritchard
rs6554348	PPAT	cis	lymphoblastoid	seeQTL
rs6554348	PPAT	cis	uninvolved skin	skin_eQTL
rs6554348	AASDH	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
2	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
3	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:57202600-57221400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
6	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
7	chr4:57203200-57235200	Weak transcription	Osteobl	bone
8	chr4:57203200-57251800	Weak transcription	A549	lung
9	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr4:57203600-57229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:57204000-57252200	Weak transcription	NH-A	brain
12	chr4:57204200-57222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:57204200-57227200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:57204800-57223400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:57204800-57235400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
18	chr4:57205000-57223000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:57205000-57228000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:57205200-57228200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:57205200-57229200	Weak transcription	Brain Germinal Matrix	brain
22	chr4:57205400-57228000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:57208800-57222800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:57210600-57222400	Weak transcription	Thymus	Thymus
26	chr4:57211000-57251600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:57211800-57252200	Weak transcription	Fetal Heart	heart
28	chr4:57212000-57221000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:57212400-57251800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:57213000-57244200	Weak transcription	Spleen	Spleen
31	chr4:57213200-57229200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr4:57213400-57251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:57213400-57252200	Weak transcription	NHLF	lung
34	chr4:57213600-57222400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr4:57213600-57223200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr4:57213600-57250200	Weak transcription	K562	blood
37	chr4:57213600-57252000	Weak transcription	HMEC	breast
38	chr4:57214400-57251800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:57214600-57252200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:57214800-57222400	Weak transcription	Lung	lung
41	chr4:57214800-57227800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr4:57214800-57229000	Weak transcription	Fetal Thymus	thymus
43	chr4:57215000-57222400	Weak transcription	Gastric	stomach
44	chr4:57215000-57222800	Weak transcription	Esophagus	oesophagus
45	chr4:57215000-57238000	Weak transcription	Brain Substantia Nigra	brain
46	chr4:57215200-57219600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:57215800-57220000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr4:57215800-57222000	Weak transcription	HSMMtube	muscle
49	chr4:57215800-57228400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:57215800-57251600	Weak transcription	Brain Anterior Caudate	brain

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