Variant report

Variant	rs1401907
Chromosome Location	chr4:57187197-57187198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57182829..57184444-chr4:57184985..57187563,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AASDH-2	chr4:57186885-57187500	NONHSAT096496

Variant related genes	Relation type
ENSG00000109265	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12501502	0.90[JPT][hapmap]
rs13147824	0.87[CEU][hapmap]
rs13147900	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1401904	0.88[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs1401906	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs1401912	0.80[CEU][hapmap]
rs1520026	0.86[JPT][hapmap]
rs1520030	0.91[JPT][hapmap]
rs2271923	0.91[JPT][hapmap]
rs2899063	0.80[CEU][hapmap];0.87[MEX][hapmap]
rs4167	0.80[CEU][hapmap];0.86[MEX][hapmap]
rs4493603	0.91[JPT][hapmap]
rs6554345	0.82[EUR][1000 genomes]
rs6554349	0.80[CEU][hapmap]
rs6554355	0.80[CEU][hapmap]
rs6554356	0.80[CEU][hapmap]
rs6826795	0.86[MEX][hapmap]
rs6834736	0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs6855041	0.91[JPT][hapmap]
rs7671868	0.91[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7683193	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7683781	0.80[CEU][hapmap];0.87[MEX][hapmap]
rs7692385	0.80[CEU][hapmap]
rs939293	0.82[EUR][1000 genomes]
rs9683679	0.80[CEU][hapmap];0.87[MEX][hapmap]
rs9684298	0.80[CEU][hapmap];0.87[MEX][hapmap]

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
rs1401907	PPAT	cis	uninvolved skin	skin_eQTL
rs1401907	PPAT	cis	lymphoblastoid	seeQTL
rs1401907	AASDH	cis	multi-tissue	Pritchard
rs1401907	AASDH	cis	parietal	SCAN
rs1401907	PPAT	cis	normal skin	skin_eQTL
rs1401907	AASDH	cis	cerebellum	SCAN
rs1401907	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57162800-57189400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr4:57167600-57203400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
4	chr4:57171000-57187400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:57172000-57204000	Weak transcription	Stomach Mucosa	stomach
6	chr4:57173200-57202800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:57174400-57195000	Strong transcription	Fetal Intestine Small	intestine
8	chr4:57174400-57203800	Weak transcription	Fetal Kidney	kidney
9	chr4:57174600-57197200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr4:57176000-57190000	Weak transcription	Gastric	stomach
11	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:57178000-57190400	Weak transcription	Brain Angular Gyrus	brain
13	chr4:57178200-57189400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:57178200-57189800	Weak transcription	Brain Anterior Caudate	brain
15	chr4:57178200-57190000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:57178200-57190200	Weak transcription	Brain Substantia Nigra	brain
17	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:57178600-57190200	Weak transcription	Fetal Brain Male	brain
19	chr4:57180400-57189800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:57180600-57190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:57180800-57191800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:57180800-57197200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:57181200-57190000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:57181200-57196400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:57181400-57203800	Weak transcription	HSMMtube	muscle
26	chr4:57181600-57189800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr4:57181800-57191200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr4:57181800-57196200	Strong transcription	Fetal Intestine Large	intestine
29	chr4:57182200-57189800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:57182800-57189600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:57182800-57196800	Weak transcription	Ovary	ovary
32	chr4:57183000-57189200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:57183000-57190200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:57183000-57193800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:57183200-57189600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:57183200-57189600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:57183200-57194400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:57183400-57189200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:57183400-57190000	Weak transcription	Colonic Mucosa	Colon
40	chr4:57183600-57188600	Weak transcription	Fetal Stomach	stomach
41	chr4:57183600-57189800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr4:57184000-57189200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:57184600-57189000	Weak transcription	Brain Germinal Matrix	brain
44	chr4:57184600-57211200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:57185000-57189600	Weak transcription	Fetal Muscle Leg	muscle
46	chr4:57185200-57188600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr4:57185200-57189400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:57185400-57188400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:57186400-57187400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:57186600-57187200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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