Variant report

Variant	rs1996650
Chromosome Location	chr4:57255073-57255074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57254214-57255273	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr4:57252843-57257309	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:57253098-57255111	K562	blood:	n/a	n/a
4	POLR2A	chr4:57253046-57257192	GM12891	blood:	n/a	n/a
5	GATA1	chr4:57253159-57256476	PBDE	blood:	n/a	chr4:57253785-57253794 chr4:57255968-57255978 chr4:57256193-57256204
6	TBL1XR1	chr4:57254651-57255236	K562	blood:	n/a	n/a
7	POLR2A	chr4:57255007-57255207	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr4:57254212-57255258	GM12878	blood:	n/a	n/a
9	ZC3H11A	chr4:57254677-57255287	K562	blood:	n/a	n/a
10	POLR2A	chr4:57253047-57255279	PBDE	blood:	n/a	n/a
11	POLR2A	chr4:57253107-57259459	K562	blood:	n/a	n/a
12	POLR2A	chr4:57253088-57255150	K562	blood:	n/a	n/a
13	POLR2A	chr4:57252965-57255539	SK-N-MC	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57252171..57255208-chr4:57332200..57335252,5	K562	blood:
2	chr4:57252130..57255932-chr4:57332416..57336369,6	K562	blood:
3	chr4:57251780..57255283-chr4:57300557..57304376,5	MCF-7	breast:
4	chr4:57254546..57256143-chr4:57396737..57398873,2	K562	blood:
5	chr4:57250870..57256510-chr4:57298204..57303491,14	K562	blood:
6	chr4:57252113..57256281-chr4:57265528..57268374,5	MCF-7	breast:
7	chr4:57252573..57255971-chr4:57298663..57303783,6	MCF-7	breast:
8	chr4:57250870..57256080-chr4:57298204..57304153,16	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAICS-3	chr4:57253640-57259528	NONHSAT096500

No data

Variant related genes	Relation type
AASDH	TF binding region
ENSG00000249693	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10031012	0.82[EUR][1000 genomes]
rs10031550	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10034154	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11133438	0.83[AFR][1000 genomes]
rs11133439	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11733474	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12331363	0.82[ASN][1000 genomes]
rs12331412	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13114104	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13133016	0.88[EUR][1000 genomes]
rs13141793	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13147824	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1356788	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1401912	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1464286	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1474178	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1976815	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2030365	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2139512	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28559894	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2899063	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796542	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796547	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3822003	0.82[EUR][1000 genomes]
rs4167	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4864581	0.83[AFR][1000 genomes]
rs4865087	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4865100	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4865101	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57503982	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59615456	0.81[EUR][1000 genomes]
rs62310633	0.82[EUR][1000 genomes]
rs6554349	0.88[EUR][1000 genomes]
rs6554352	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6554355	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554356	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6812041	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6826795	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6841016	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6841053	0.84[ASN][1000 genomes]
rs6856845	0.80[EUR][1000 genomes]
rs7657711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7661712	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7683781	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7692385	0.87[EUR][1000 genomes]
rs7693683	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9312674	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9683679	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9684298	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9997639	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1996650	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs1996650	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57252200-57255200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:57252200-57255200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:57252200-57255200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr4:57252400-57255200	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:57252400-57255400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:57252400-57255600	Active TSS	K562	blood
7	chr4:57252600-57255400	Active TSS	GM12878-XiMat	blood
8	chr4:57252600-57255400	Active TSS	NHDF-Ad	bronchial
9	chr4:57253800-57255200	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr4:57253800-57255200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:57254000-57255200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
13	chr4:57254400-57255200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:57254400-57255200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:57254400-57255200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:57254400-57255200	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr4:57254400-57255200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:57254400-57255200	Flanking Active TSS	Colon Smooth Muscle	Colon
19	chr4:57254400-57255200	Flanking Active TSS	Osteobl	bone
20	chr4:57254400-57255400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:57254400-57255400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr4:57254400-57255400	Flanking Active TSS	Dnd41	blood
23	chr4:57254400-57256400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:57254400-57268400	Weak transcription	Lung	lung
25	chr4:57254400-57273600	Weak transcription	Pancreas	Pancrea
26	chr4:57254600-57255200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:57254600-57255200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:57254600-57255200	Flanking Active TSS	HMEC	breast
29	chr4:57254600-57255400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:57254600-57255400	Flanking Active TSS	HepG2	liver
31	chr4:57254600-57255600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr4:57254600-57255800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr4:57254600-57264000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:57254600-57271600	Weak transcription	Ovary	ovary
35	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
36	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:57254800-57255200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:57254800-57255200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:57254800-57255200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:57254800-57255200	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr4:57254800-57255200	Active TSS	Muscle Satellite Cultured Cells	--
42	chr4:57254800-57255200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:57254800-57255200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr4:57254800-57255200	Enhancers	Fetal Heart	heart
45	chr4:57254800-57255200	Enhancers	Fetal Intestine Large	intestine
46	chr4:57254800-57255200	Enhancers	Fetal Lung	lung
47	chr4:57254800-57255200	Enhancers	Fetal Stomach	stomach
48	chr4:57254800-57255200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr4:57254800-57255200	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr4:57254800-57255400	Enhancers	Primary T cells from cord blood	blood

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