Variant report

Variant	rs437876
Chromosome Location	chr3:42568440-42568441
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	GABPA	chr3:42568150-42568444	K562	blood:	n/a	n/a
2	CTCF	chr3:42568320-42568470	NHEK	skin:	n/a	n/a
3	MYC	chr3:42568070-42568849	NB4	blood:	n/a	chr3:42568557-42568566
4	MAX	chr3:42567999-42568924	NB4	blood:	n/a	chr3:42568557-42568566
5	CTCF	chr3:42568260-42568530	GM12869	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42566788..42568912-chr3:42571807..42573949,2	K562	blood:
2	chr3:42555090..42557381-chr3:42567941..42570291,2	MCF-7	breast:

Variant related genes	Relation type
VIPR1	TF binding region
ENSG00000232354	Chromatin interaction
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17237090	0.80[JPT][hapmap]
rs8913	0.87[JPT][hapmap]

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	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs437876	SS18L2	cis	cerebellum	SCAN
rs437876	VIPR1	cis	cerebellum	SCAN
rs437876	MOBP	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:42552200-42581000	Weak transcription	Pancreas	Pancrea
3	chr3:42552400-42570000	Weak transcription	Fetal Stomach	stomach
4	chr3:42557600-42569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:42557600-42571600	Weak transcription	Brain Angular Gyrus	brain
6	chr3:42557600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:42557600-42574400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:42557800-42586000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:42557800-42590400	Weak transcription	Aorta	Aorta
10	chr3:42558000-42570200	Weak transcription	Adipose Nuclei	Adipose
11	chr3:42558000-42573000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:42558000-42585200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:42560200-42573400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:42561000-42581000	Weak transcription	Gastric	stomach
15	chr3:42561400-42570400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr3:42561800-42568600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:42562400-42570800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:42562400-42586800	Weak transcription	Small Intestine	intestine
19	chr3:42562800-42574200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:42563000-42572400	Weak transcription	Right Ventricle	heart
21	chr3:42563600-42575000	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr3:42564000-42577400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr3:42564400-42570600	Genic enhancers	Lung	lung
24	chr3:42565200-42576400	Enhancers	Spleen	Spleen
25	chr3:42565600-42570400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:42565800-42570000	Strong transcription	Colonic Mucosa	Colon
27	chr3:42566000-42571800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr3:42566200-42571200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:42566200-42571400	Enhancers	Fetal Thymus	thymus
30	chr3:42566400-42571000	Enhancers	Primary T cells fromperipheralblood	blood
31	chr3:42566600-42571200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:42566600-42571400	Weak transcription	Brain Anterior Caudate	brain
33	chr3:42566800-42570400	Weak transcription	Liver	Liver
34	chr3:42567000-42568600	Enhancers	Placenta	Placenta
35	chr3:42567000-42571000	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr3:42567200-42570800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr3:42567200-42571000	Weak transcription	Right Atrium	heart
38	chr3:42567200-42573000	Weak transcription	Esophagus	oesophagus
39	chr3:42567400-42570200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:42567400-42571400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:42567600-42569400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr3:42567600-42570800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr3:42567600-42573800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr3:42567600-42580200	Strong transcription	Fetal Intestine Small	intestine
45	chr3:42567800-42568600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:42567800-42568800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr3:42567800-42570600	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr3:42567800-42572600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:42567800-42577200	Strong transcription	Fetal Intestine Large	intestine
50	chr3:42568000-42568800	Enhancers	Thymus	Thymus

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