Variant report

Variant	rs6854326
Chromosome Location	chr4:57275909-57275910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr4:57274987-57277307	SK-N-SH	brain:	n/a	chr4:57276622-57276637 chr4:57276620-57276635

No.	Distal block	Cell Line	Cell type
1	chr4:57275040..57277242-chr4:57300118..57301937,2	MCF-7	breast:
2	chr4:57274956..57277925-chr4:57332751..57335099,2	MCF-7	breast:
3	chr4:57275711..57277429-chr4:57298915..57301727,2	K562	blood:

Variant related genes	Relation type
PPAT	TF binding region
ENSG00000268171	TF binding region
ENSG00000128059	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1042040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1124570	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11538098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11722404	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11728068	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11732985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11734595	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11935357	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11937997	0.88[EUR][1000 genomes]
rs11943048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11946745	0.84[EUR][1000 genomes]
rs13109030	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13114481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13122196	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13122422	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13122832	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13123301	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs13123542	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13124065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13129188	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13131846	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13132553	0.91[EUR][1000 genomes]
rs13134963	0.81[CEU][hapmap]
rs13135151	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13140746	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13146014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13148435	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13148656	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13150137	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13150967	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1401908	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1401911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2030363	0.92[EUR][1000 genomes]
rs2176785	0.81[CEU][hapmap]
rs3796544	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6554346	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6554347	0.83[CEU][hapmap]
rs6554350	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6554353	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6554354	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6811153	0.91[EUR][1000 genomes]
rs6811616	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs6811652	0.92[EUR][1000 genomes]
rs6812222	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6815480	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6818283	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6818340	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6820922	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6857561	0.91[EUR][1000 genomes]
rs7437329	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7654543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7656361	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7673373	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7682041	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7682608	0.91[EUR][1000 genomes]
rs7695701	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs7699157	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs956275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9995463	0.91[CEU][hapmap];0.90[EUR][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	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
4	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
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6854326	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs6854326	AASDH	cis	multi-tissue	Pritchard
rs6854326	AASDH	cis	Skin Sun Exposed Lower leg	GTEx
rs6854326	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
2	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
5	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
6	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:57255200-57276400	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:57255200-57276600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:57255200-57276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:57255200-57276600	Weak transcription	Brain Substantia Nigra	brain
11	chr4:57255400-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:57255800-57276600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:57256000-57276400	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:57256200-57276600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:57256400-57276600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
17	chr4:57264400-57276400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:57267600-57276000	Weak transcription	Brain Anterior Caudate	brain
21	chr4:57267600-57276200	Weak transcription	HSMM	muscle
22	chr4:57267600-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:57267800-57277600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr4:57267800-57278400	Weak transcription	Placenta	Placenta
25	chr4:57270200-57276800	Weak transcription	Colonic Mucosa	Colon
26	chr4:57272000-57276200	Weak transcription	Fetal Intestine Large	intestine
27	chr4:57272000-57276400	Weak transcription	HSMMtube	muscle
28	chr4:57272200-57276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:57272200-57276400	Weak transcription	Aorta	Aorta
30	chr4:57272200-57276400	Weak transcription	Ovary	ovary
31	chr4:57272200-57276600	Weak transcription	Fetal Intestine Small	intestine
32	chr4:57272400-57276600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:57272600-57276200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:57272600-57276400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:57272600-57276400	Weak transcription	Adipose Nuclei	Adipose
36	chr4:57272600-57276600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:57272600-57280200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:57272800-57276200	Weak transcription	Liver	Liver
39	chr4:57272800-57276200	Weak transcription	Fetal Muscle Leg	muscle
40	chr4:57272800-57276600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:57272800-57276600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:57272800-57276600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr4:57272800-57280400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr4:57272800-57281600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr4:57272800-57292600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
47	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
48	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:57273000-57276400	Weak transcription	HepG2	liver
50	chr4:57273000-57276800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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