Variant report

Variant	rs3774790
Chromosome Location	chr3:43750108-43750109
allele	A/C/G/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	MYC	chr3:43749423-43751067	MCF10A-Er-Src	breast:	n/a	chr3:43749753-43749764 chr3:43750667-43750677
2	FOS	chr3:43749407-43750918	MCF10A-Er-Src	breast:	n/a	chr3:43749747-43749756 chr3:43749748-43749755 chr3:43749748-43749757 chr3:43749746-43749757 chr3:43749747-43749757
3	MYC	chr3:43749423-43751117	MCF10A-Er-Src	breast:	n/a	chr3:43749753-43749764 chr3:43750667-43750677
4	TCF12	chr3:43749373-43750126	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:43749325-43751266	K562	blood:	n/a	n/a
6	STAT3	chr3:43750050-43750219	MCF10A-Er-Src	breast:	n/a	n/a
7	GATA3	chr3:43749317-43750133	SK-N-SH	brain:	n/a	n/a
8	RCOR1	chr3:43749193-43750191	IMR90	lung:	n/a	n/a
9	JUND	chr3:43749253-43750171	SK-N-SH	brain:	n/a	chr3:43749747-43749756 chr3:43749748-43749755 chr3:43749746-43749757 chr3:43749748-43749757 chr3:43749747-43749757
10	GATA3	chr3:43749271-43750185	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:43748995..43751917-chr3:43764749..43767365,2	K562	blood:
2	chr3:43734084..43735791-chr3:43750065..43752482,2	MCF-7	breast:
3	chr3:43731020..43735368-chr3:43749595..43752520,5	K562	blood:
4	chr3:43749486..43751869-chr3:43752824..43755370,3	K562	blood:
5	chr3:43729847..43733891-chr3:43748339..43751413,6	MCF-7	breast:
6	chr3:43712776..43714761-chr3:43748977..43750830,2	K562	blood:

Variant related genes	Relation type
ABHD5	TF binding region
ENSG00000011198	Chromatin interaction
ENSG00000160746	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1021049	0.85[CHD][hapmap]
rs1038202	0.85[CHD][hapmap]
rs11714015	0.85[CHD][hapmap]
rs13092838	0.85[CHD][hapmap]
rs1482651	0.85[CHD][hapmap]
rs1482652	0.85[CHD][hapmap]
rs17075971	0.85[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs2054554	0.85[CHD][hapmap]
rs2170219	0.85[CHD][hapmap]
rs3733155	0.83[CEU][hapmap]
rs3755602	0.85[CHD][hapmap]
rs3772165	0.85[CHD][hapmap]
rs3774792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821381	0.85[CHD][hapmap]
rs4234430	0.90[CHB][hapmap]
rs4325902	0.82[ASN][1000 genomes]
rs4432612	0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4682690	0.85[CHD][hapmap]
rs4682691	0.84[CHD][hapmap]
rs4682892	0.85[CHD][hapmap]
rs4682900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56136723	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441786	0.85[CHD][hapmap]
rs6441787	1.00[CHB][hapmap]
rs6809134	0.85[CHD][hapmap]
rs73089215	0.91[ASN][1000 genomes]
rs7428158	0.84[CHD][hapmap]
rs7616708	0.85[CHD][hapmap]
rs7621271	0.85[CHD][hapmap]
rs7630010	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs7653738	0.85[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834673	chr3:43622985-43799876	Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3774790	NKTR	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43733400-43753200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:43733400-43767800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:43733600-43753600	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:43733600-43767400	Weak transcription	Fetal Brain Male	brain
5	chr3:43733600-43768000	Weak transcription	Fetal Kidney	kidney
6	chr3:43734000-43751800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:43734000-43753200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:43734200-43753600	Weak transcription	Primary T cells from cord blood	blood
9	chr3:43734200-43753600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:43734200-43754800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:43734400-43751800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:43734400-43753200	Weak transcription	Fetal Thymus	thymus
13	chr3:43734400-43753200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:43734400-43753200	Weak transcription	HSMMtube	muscle
15	chr3:43734400-43762200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:43734600-43751800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:43734600-43753200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:43734600-43753200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:43734600-43753400	Weak transcription	Fetal Brain Female	brain
20	chr3:43734800-43753600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:43734800-43774400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:43735000-43753200	Weak transcription	Right Ventricle	heart
23	chr3:43735000-43761200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:43735200-43753400	Weak transcription	Brain Anterior Caudate	brain
25	chr3:43738000-43762200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:43738200-43753200	Weak transcription	Fetal Lung	lung
27	chr3:43738400-43753400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:43738400-43753600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:43738600-43753200	Weak transcription	Gastric	stomach
30	chr3:43738600-43753400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:43738600-43763600	Weak transcription	Small Intestine	intestine
32	chr3:43738800-43753600	Weak transcription	Psoas Muscle	Psoas
33	chr3:43738800-43763600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:43740400-43762000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:43740600-43753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:43740600-43753400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:43741000-43768000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:43741600-43762200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:43744200-43750400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:43744200-43752800	Weak transcription	Dnd41	blood
41	chr3:43744200-43753000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:43744200-43753200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:43744200-43753200	Weak transcription	Aorta	Aorta
44	chr3:43744200-43753200	Weak transcription	Thymus	Thymus
45	chr3:43744200-43753600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr3:43744200-43753600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:43744400-43752800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:43744400-43753200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:43744400-43753200	Weak transcription	Colonic Mucosa	Colon
50	chr3:43744400-43753400	Weak transcription	Stomach Smooth Muscle	stomach

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