Variant report

Variant	rs2176785
Chromosome Location	chr4:57276739-57276740
allele	C/G
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	MAX	chr4:57276285-57276890	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr4:57276349-57276820	MCF-7	breast:	n/a	n/a
3	POLR2A	chr4:57276448-57276874	U87	brain:	n/a	n/a
4	POLR2A	chr4:57276368-57276901	H1-neurons	neurons:	n/a	n/a
5	FOXA2	chr4:57276484-57276783	A549	lung:	n/a	n/a
6	NR2C2	chr4:57276508-57276834	Hela-S3	cervix:	n/a	chr4:57276664-57276673
7	STAT3	chr4:57276104-57276886	MCF10A-Er-Src	breast:	n/a	chr4:57276647-57276654
8	SIN3AK20	chr4:57276470-57276779	SK-N-SH	brain:	n/a	n/a
9	ATF2	chr4:57276366-57276850	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYC	chr4:57276393-57276772	MCF10A-Er-Src	breast:	n/a	n/a
11	GABPA	chr4:57276152-57277216	MCF-7	breast:	n/a	n/a
12	GATA3	chr4:57276313-57276742	T-47D	breast:	n/a	n/a
13	PBX3	chr4:57276246-57276929	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr4:57276299-57277134	H1-neurons	neurons:	n/a	n/a
15	FOSL1	chr4:57276367-57276974	HCT-116	colon:	n/a	n/a
16	FOXA1	chr4:57276444-57276826	HepG2	liver:	n/a	n/a
17	POLR2A	chr4:57276487-57276774	SK-N-SH	brain:	n/a	n/a
18	TCF12	chr4:57276471-57276743	H1-hESC	embryonic stem cell:	n/a	n/a
19	JUND	chr4:57276400-57276834	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:57276332-57276943	MCF10A-Er-Src	breast:	n/a	n/a
21	GATA3	chr4:57276197-57276910	MCF-7	breast:	n/a	n/a
22	JUN	chr4:57276446-57276806	H1-hESC	embryonic stem cell:	n/a	n/a
23	STAT3	chr4:57276435-57276828	MCF10A-Er-Src	breast:	n/a	chr4:57276647-57276654
24	REST	chr4:57276308-57276980	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr4:57276622-57276910	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr4:57276369-57276940	IMR90	lung:	n/a	n/a
27	JUND	chr4:57276470-57276843	K562	blood:	n/a	n/a
28	HDAC2	chr4:57276300-57276823	MCF-7	breast:	n/a	chr4:57276401-57276415
29	YY1	chr4:57276391-57276832	SK-N-SH_RA	brain:	n/a	chr4:57276609-57276628
30	JUN	chr4:57276317-57276845	HUVEC	blood vessel:	n/a	n/a
31	STAT3	chr4:57276417-57276827	MCF10A-Er-Src	breast:	n/a	chr4:57276647-57276654
32	SIN3A	chr4:57276420-57276790	H1-hESC	embryonic stem cell:	n/a	n/a
33	STAT3	chr4:57276435-57276878	MCF10A-Er-Src	breast:	n/a	chr4:57276647-57276654
34	PBX3	chr4:57276352-57276878	SK-N-SH	brain:	n/a	n/a
35	NR2C2	chr4:57276496-57276810	HepG2	liver:	n/a	chr4:57276664-57276673
36	FOS	chr4:57276195-57276903	HUVEC	blood vessel:	n/a	n/a
37	FOSL2	chr4:57276422-57276873	SK-N-SH	brain:	n/a	n/a
38	YY1	chr4:57276511-57276862	ECC-1	luminal epithelium:	n/a	chr4:57276609-57276628
39	MAX	chr4:57276441-57276739	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr4:57276403-57276843	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr4:57276431-57276824	PFSK-1	brain:	n/a	n/a
42	YY1	chr4:57276481-57276769	HCT-116	colon:	n/a	chr4:57276609-57276628
43	TAF1	chr4:57276454-57276828	SK-N-SH	brain:	n/a	n/a
44	SP1	chr4:57276336-57276906	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAX	chr4:57276506-57276778	Hela-S3	cervix:	n/a	n/a
46	JUND	chr4:57276466-57276829	HepG2	liver:	n/a	n/a
47	EP300	chr4:57276468-57276776	SK-N-SH_RA	brain:	n/a	n/a
48	YY1	chr4:57276459-57276872	ECC-1	luminal epithelium:	n/a	chr4:57276609-57276628
49	CHD1	chr4:57276634-57277088	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr4:57276458-57276831	MCF-7	breast:	n/a	n/a

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
ENSG00000128059	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000174780	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11728110	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11732985	0.80[CEU][hapmap]
rs11930159	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11934636	0.83[JPT][hapmap]
rs12644498	0.84[JPT][hapmap]
rs12650288	0.83[JPT][hapmap]
rs13102012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13102298	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13109030	0.86[CEU][hapmap]
rs13114481	0.80[CEU][hapmap]
rs13122196	0.86[CEU][hapmap]
rs13122832	0.86[CEU][hapmap]
rs13124696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13129188	0.86[CEU][hapmap]
rs13134963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13135046	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13146014	0.80[CEU][hapmap]
rs13147132	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13148656	0.85[CEU][hapmap]
rs13150159	0.85[EUR][1000 genomes]
rs13150967	0.85[CEU][hapmap]
rs1401911	0.80[CEU][hapmap]
rs1579019	0.83[JPT][hapmap]
rs17086759	0.92[JPT][hapmap]
rs17086773	0.92[JPT][hapmap]
rs17086801	0.84[JPT][hapmap]
rs17086804	0.83[JPT][hapmap]
rs17086830	0.83[JPT][hapmap]
rs17086838	0.84[JPT][hapmap]
rs2030364	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3733324	0.83[JPT][hapmap]
rs3733326	0.92[JPT][hapmap]
rs3796540	0.91[JPT][hapmap]
rs3796544	0.85[CEU][hapmap]
rs3796550	0.83[JPT][hapmap]
rs4076103	0.84[JPT][hapmap]
rs41498446	0.83[JPT][hapmap]
rs6554347	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554350	0.86[CEU][hapmap]
rs6554354	0.85[CEU][hapmap]
rs6811616	0.85[CEU][hapmap]
rs6812222	0.85[CEU][hapmap]
rs6830145	0.84[JPT][hapmap]
rs6854326	0.81[CEU][hapmap]
rs6854758	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7437329	0.80[CEU][hapmap]
rs7654543	0.80[CEU][hapmap]
rs7694439	0.95[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9995463	0.85[CEU][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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2176785	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs2176785	AASDH	cis	lung	GTEx
rs2176785	AASDH	cis	multi-tissue	Pritchard
rs2176785	AASDH	cis	Skin Sun Exposed Lower leg	GTEx
rs2176785	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
4	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:57267800-57277600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:57267800-57278400	Weak transcription	Placenta	Placenta
8	chr4:57270200-57276800	Weak transcription	Colonic Mucosa	Colon
9	chr4:57272600-57280200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:57272800-57280400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:57272800-57281600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr4:57272800-57292600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
14	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
15	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:57273000-57276800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:57273200-57276800	Weak transcription	Hela-S3	cervix
18	chr4:57274000-57287000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:57274000-57290600	Weak transcription	GM12878-XiMat	blood
20	chr4:57274200-57276800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:57274200-57287000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr4:57274200-57296400	Weak transcription	Dnd41	blood
23	chr4:57275000-57278200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr4:57275000-57278400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr4:57275200-57278000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr4:57275400-57277800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:57275400-57278200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:57275400-57278200	Enhancers	NHDF-Ad	bronchial
29	chr4:57275600-57277000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:57275600-57277600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:57276000-57277200	Flanking Active TSS	HUVEC	blood vessel
32	chr4:57276200-57276800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:57276200-57276800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:57276200-57276800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:57276200-57276800	Active TSS	HMEC	breast
36	chr4:57276200-57276800	Active TSS	NHLF	lung
37	chr4:57276200-57277000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:57276200-57277000	Enhancers	Liver	Liver
39	chr4:57276200-57277000	Active TSS	Fetal Muscle Leg	muscle
40	chr4:57276200-57277000	Active TSS	Fetal Stomach	stomach
41	chr4:57276200-57277000	Active TSS	Stomach Smooth Muscle	stomach
42	chr4:57276200-57277000	Flanking Active TSS	NH-A	brain
43	chr4:57276200-57277200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:57276200-57277200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:57276200-57277200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr4:57276200-57277200	Flanking Active TSS	Osteobl	bone
47	chr4:57276200-57278000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:57276200-57278000	Active TSS	Brain Anterior Caudate	brain
49	chr4:57276200-57280200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:57276400-57276800	Active TSS	ES-I3 Cell Line	embryonic stem cell

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