Variant report

Variant	rs3732869
Chromosome Location	chr3:141295778-141295779
allele	A/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	CTCF	chr3:141295760-141295910	NHDF-neo	bronchial:	n/a	n/a
2	CTCF	chr3:141295740-141295890	AG10803	skin:	n/a	n/a
3	RAD21	chr3:141294988-141295865	SK-N-SH	brain:	n/a	chr3:141295503-141295522 chr3:141295504-141295513
4	CTCF	chr3:141294913-141295848	A549	lung:	n/a	chr3:141295504-141295525 chr3:141295506-141295513 chr3:141295110-141295118 chr3:141295502-141295520
5	RAD21	chr3:141295242-141295791	HCT-116	colon:	n/a	chr3:141295503-141295522 chr3:141295504-141295513
6	CTCF	chr3:141295019-141295881	SK-N-SH	brain:	n/a	chr3:141295504-141295525 chr3:141295506-141295513 chr3:141295110-141295118 chr3:141295502-141295520

No.	Distal block	Cell Line	Cell type
1	chr3:141295214..141296097-chr3:141456865..141457530,2	K562	blood:
2	chr3:141000930..141002501-chr3:141293837..141295898,2	K562	blood:
3	chr3:141295052..141295995-chr3:141363331..141364146,2	MCF-7	breast:
4	chr3:141295275..141295993-chr3:141593960..141594866,2	MCF-7	breast:
5	chr3:141295145..141295891-chr3:141456926..141457444,2	MCF-7	breast:

Variant related genes	Relation type
RASA2	TF binding region
ENSG00000114125	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11711375	0.88[JPT][hapmap]
rs11917587	0.89[JPT][hapmap]
rs12107989	0.81[YRI][hapmap]
rs1493209	0.89[JPT][hapmap]
rs1493210	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16851438	0.84[JPT][hapmap]
rs16851441	1.00[JPT][hapmap]
rs16851483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1863867	0.89[JPT][hapmap]
rs2035935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2035936	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312193	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2639997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2640017	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295299	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295300	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs295320	0.88[JPT][hapmap]
rs295321	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295323	0.88[JPT][hapmap]
rs295324	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34558081	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806646	0.89[JPT][hapmap]
rs3806648	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821710	0.88[JPT][hapmap]
rs3821712	0.88[JPT][hapmap]
rs4683404	0.88[JPT][hapmap]
rs4683610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683612	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58025624	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60654199	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61750362	0.86[AFR][1000 genomes]
rs6767158	0.88[JPT][hapmap]
rs6785874	0.88[JPT][hapmap]
rs6795168	0.89[JPT][hapmap]
rs6800122	0.88[JPT][hapmap]
rs6808837	0.88[JPT][hapmap]
rs73871847	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7618787	0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs7626871	0.89[JPT][hapmap]
rs7627774	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7627807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7643837	0.88[JPT][hapmap]
rs9878347	0.84[JPT][hapmap]
rs9879503	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006237	chr3:141227525-141300722	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1795799	chr3:141284383-141301451	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1794809	chr3:141290177-141304631	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3732869	ZBTB38	cis	Lymphoblastoid	GTEx
rs3732869	ZBTB38	cis	multi-tissue	Pritchard
rs3732869	ZBTB38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141236400-141301000	Weak transcription	Brain Substantia Nigra	brain
2	chr3:141236400-141306600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:141236600-141297000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:141236600-141299400	Weak transcription	Gastric	stomach
5	chr3:141237000-141299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:141243400-141299400	Weak transcription	Spleen	Spleen
7	chr3:141254800-141299200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:141254800-141299400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:141254800-141299400	Weak transcription	Right Ventricle	heart
10	chr3:141254800-141319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:141255200-141304800	Weak transcription	Ovary	ovary
12	chr3:141255200-141320000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:141255400-141319200	Weak transcription	Aorta	Aorta
14	chr3:141257000-141300200	Weak transcription	Pancreas	Pancrea
15	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
16	chr3:141268400-141297800	Weak transcription	Fetal Heart	heart
17	chr3:141271200-141299400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:141272600-141319200	Strong transcription	Dnd41	blood
19	chr3:141275800-141320600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:141276000-141299400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:141276200-141297000	Weak transcription	Lung	lung
22	chr3:141276400-141329400	Weak transcription	Small Intestine	intestine
23	chr3:141277200-141297000	Weak transcription	Thymus	Thymus
24	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:141277600-141296400	Weak transcription	Hela-S3	cervix
26	chr3:141277800-141312000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:141278000-141296800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:141281800-141297000	Weak transcription	Fetal Intestine Small	intestine
29	chr3:141281800-141329400	Weak transcription	Fetal Brain Male	brain
30	chr3:141284600-141299200	Weak transcription	Fetal Stomach	stomach
31	chr3:141288000-141312400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:141288200-141320000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:141288400-141316400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:141288600-141302800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:141288600-141308400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:141288600-141316400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr3:141288800-141299800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:141289000-141311800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:141289000-141316600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr3:141289200-141309000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:141289200-141316400	Strong transcription	Fetal Thymus	thymus
42	chr3:141289400-141301600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:141290200-141301600	Strong transcription	NH-A	brain
44	chr3:141290400-141299400	Weak transcription	Brain Anterior Caudate	brain
45	chr3:141290600-141297200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:141291000-141301200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:141291200-141297200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:141291600-141297000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:141291600-141299200	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:141292400-141297000	Weak transcription	HSMMtube	muscle

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