Variant report

Variant	rs1546737
Chromosome Location	chr3:52407041-52407042
allele	A/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	POLR2A	chr3:52406854-52407475	HL-60	blood:	n/a	n/a
2	SPI1	chr3:52406946-52407540	GM12878	blood:	n/a	chr3:52407276-52407289
3	ELF1	chr3:52406762-52407468	GM12878	blood:	n/a	chr3:52407241-52407253 chr3:52407239-52407248
4	SPI1	chr3:52407024-52407564	HL-60	blood:	n/a	chr3:52407276-52407289
5	MAX	chr3:52406964-52407422	NB4	blood:	n/a	chr3:52407204-52407214
6	POLR2A	chr3:52406648-52407547	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52272390..52274822-chr3:52406008..52407949,2	K562	blood:
2	chr3:52406156..52409184-chr3:52415561..52421026,5	K562	blood:
3	chr3:52321755..52323526-chr3:52405745..52408434,2	K562	blood:
4	chr3:52406883..52409184-chr3:52415694..52419355,3	K562	blood:
5	chr3:52018451..52021014-chr3:52404106..52407054,2	K562	blood:

Variant related genes	Relation type
ENSG00000239557	TF binding region
ENSG00000164091	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000239732	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12636502	1.00[LWK][hapmap]
rs13094687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2267847	0.82[EUR][1000 genomes]
rs2272088	1.00[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs34228726	0.91[EUR][1000 genomes]
rs34569561	1.00[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs3844291	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs3852063	0.93[EUR][1000 genomes]
rs3852064	1.00[CEU][hapmap];0.92[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs57615517	0.90[EUR][1000 genomes]
rs57630131	0.85[EUR][1000 genomes]
rs59565798	0.92[EUR][1000 genomes]
rs731831	0.90[CEU][hapmap]
rs7618915	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv979833	chr3:52387550-52407592	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs1546737	SPCS1	cis	parietal	SCAN
rs1546737	ITIH4-AS1	cis	Artery Aorta	GTEx
rs1546737	ITIH3	cis	parietal	SCAN
rs1546737	CACNA2D3	cis	parietal	SCAN
rs1546737	RBM6	cis	cerebellum	SCAN
rs1546737	GNL3	cis	parietal	SCAN
rs1546737	NEK4	cis	cerebellum	SCAN
rs1546737	NT5DC2	cis	parietal	SCAN
rs1546737	NEK4	cis	parietal	SCAN
rs1546737	PRKCD	cis	parietal	SCAN
rs1546737	GNL3	cis	cerebellum	SCAN
rs1546737	ITIH4	cis	cerebellum	SCAN
rs1546737	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs1546737	ITIH4	cis	parietal	SCAN
rs1546737	TMEM110	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:52377800-52407200	Strong transcription	Fetal Intestine Large	intestine
3	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:52381400-52407400	Weak transcription	NHLF	lung
5	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
6	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
8	chr3:52395200-52407200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:52395400-52409400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
11	chr3:52397400-52407400	Weak transcription	Fetal Lung	lung
12	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:52398000-52407400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
15	chr3:52399000-52409400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:52399400-52409400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:52400200-52409200	Weak transcription	Right Ventricle	heart
18	chr3:52401000-52409400	Weak transcription	Esophagus	oesophagus
19	chr3:52401200-52409400	Weak transcription	Colonic Mucosa	Colon
20	chr3:52403000-52407600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:52403200-52407600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
23	chr3:52404800-52409200	Weak transcription	Pancreas	Pancrea
24	chr3:52405000-52407400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:52405000-52408400	Weak transcription	Brain Substantia Nigra	brain
26	chr3:52405000-52409200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:52405000-52409200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:52405000-52409400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:52405000-52409400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:52405200-52425000	Weak transcription	Aorta	Aorta
31	chr3:52405400-52425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:52405600-52409200	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:52405600-52409200	Weak transcription	Lung	lung
34	chr3:52405800-52407200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:52406200-52407400	Enhancers	Primary B cells from cord blood	blood
36	chr3:52406200-52409200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:52406200-52409400	Enhancers	GM12878-XiMat	blood
38	chr3:52406400-52407200	Enhancers	Spleen	Spleen
39	chr3:52406400-52407400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:52406400-52407600	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr3:52406400-52407600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:52406400-52408000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:52406400-52408000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr3:52406400-52408000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:52406400-52409400	Weak transcription	Brain Anterior Caudate	brain
46	chr3:52406400-52409400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:52406400-52425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:52406600-52407200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:52406600-52407200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:52406600-52407400	Weak transcription	Adipose Nuclei	Adipose

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