Variant report

Variant	rs6554349
Chromosome Location	chr4:57222781-57222782
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA1211-1	chr4:57222301-57223098	NONHSAT096499

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10031012	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10031550	0.90[EUR][1000 genomes]
rs11133438	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11133439	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][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]
rs11610	0.95[JPT][hapmap]
rs11724302	0.88[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11733474	0.87[CEU][hapmap]
rs12646703	1.00[JPT][hapmap]
rs13114104	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13133016	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138648	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13141793	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13147824	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1356787	0.95[JPT][hapmap]
rs1356788	0.88[EUR][1000 genomes]
rs1401907	0.80[CEU][hapmap]
rs1401912	1.00[CEU][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs1464286	0.89[EUR][1000 genomes]
rs1976815	0.89[EUR][1000 genomes]
rs1996650	0.88[EUR][1000 genomes]
rs2030362	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2030365	0.89[EUR][1000 genomes]
rs2139512	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2292985	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28559894	0.81[EUR][1000 genomes]
rs2899063	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3796542	0.89[EUR][1000 genomes]
rs3796547	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs3822003	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs4167	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4864578	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4864581	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865087	0.90[EUR][1000 genomes]
rs4865090	0.86[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]
rs4865100	0.85[EUR][1000 genomes]
rs4865101	0.89[EUR][1000 genomes]
rs57503982	0.81[EUR][1000 genomes]
rs62310633	0.80[EUR][1000 genomes]
rs6554348	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]
rs6554352	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6554355	1.00[CEU][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes]
rs6554356	1.00[CEU][hapmap];0.88[YRI][hapmap];0.89[EUR][1000 genomes]
rs6584	0.95[JPT][hapmap]
rs6812041	0.89[EUR][1000 genomes]
rs6816268	0.96[JPT][hapmap]
rs6826795	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs6830518	0.95[JPT][hapmap]
rs6834736	0.89[YRI][hapmap]
rs6836864	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6841016	0.84[EUR][1000 genomes]
rs6848187	0.95[JPT][hapmap]
rs6856845	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7657711	0.89[EUR][1000 genomes]
rs7661712	0.89[EUR][1000 genomes]
rs7683781	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7689163	0.91[JPT][hapmap]
rs7692385	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]
rs7693137	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]
rs7693683	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9312673	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9683679	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes]
rs9684298	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes]
rs9762333	0.80[AMR][1000 genomes]
rs9993277	0.83[CEU][hapmap]
rs9997639	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv964045	chr4:57221208-57226954	Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6554349	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs6554349	PPAT	cis	normal skin	skin_eQTL
rs6554349	PPAT	cis	lesional skin	skin_eQTL
rs6554349	PPAT	cis	uninvolved skin	skin_eQTL
rs6554349	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 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	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
5	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
6	chr4:57203200-57235200	Weak transcription	Osteobl	bone
7	chr4:57203200-57251800	Weak transcription	A549	lung
8	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:57203600-57229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:57204000-57252200	Weak transcription	NH-A	brain
11	chr4:57204200-57227200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:57204800-57223400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:57204800-57235400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
16	chr4:57205000-57223000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:57205000-57228000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:57205200-57228200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:57205200-57229200	Weak transcription	Brain Germinal Matrix	brain
20	chr4:57205400-57228000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:57208800-57222800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:57211000-57251600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:57211800-57252200	Weak transcription	Fetal Heart	heart
25	chr4:57212400-57251800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:57213000-57244200	Weak transcription	Spleen	Spleen
27	chr4:57213200-57229200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr4:57213400-57251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:57213400-57252200	Weak transcription	NHLF	lung
30	chr4:57213600-57223200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr4:57213600-57250200	Weak transcription	K562	blood
32	chr4:57213600-57252000	Weak transcription	HMEC	breast
33	chr4:57214400-57251800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:57214600-57252200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:57214800-57227800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:57214800-57229000	Weak transcription	Fetal Thymus	thymus
37	chr4:57215000-57222800	Weak transcription	Esophagus	oesophagus
38	chr4:57215000-57238000	Weak transcription	Brain Substantia Nigra	brain
39	chr4:57215800-57228400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:57215800-57251600	Weak transcription	Brain Anterior Caudate	brain
41	chr4:57216000-57223200	Weak transcription	Fetal Kidney	kidney
42	chr4:57216000-57228800	Weak transcription	Dnd41	blood
43	chr4:57216000-57235800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:57216000-57236400	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:57216000-57241200	Weak transcription	Pancreas	Pancrea
46	chr4:57216000-57251800	Weak transcription	HepG2	liver
47	chr4:57216000-57252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:57216000-57253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:57216200-57224400	Weak transcription	Brain Angular Gyrus	brain
50	chr4:57216200-57226200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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