Variant report

Variant	rs9855938
Chromosome Location	chr3:46957298-46957299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46955122..46957906-chr3:46963303..46965822,3	K562	blood:
2	chr3:46952895..46958117-chr3:46959206..46961896,4	K562	blood:
3	chr3:46956820..46959404-chr3:47037411..47039002,2	K562	blood:
4	chr3:46956501..46959186-chr3:47021476..47023726,2	K562	blood:

Variant related genes	Relation type
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1001284	0.94[ASN][1000 genomes]
rs10461018	0.87[JPT][hapmap]
rs1079276	0.81[JPT][hapmap]
rs10865943	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130110	0.87[JPT][hapmap]
rs11130111	0.86[JPT][hapmap]
rs1138518	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs11705936	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719795	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs11926707	0.80[CEU][hapmap]
rs13061071	0.81[JPT][hapmap]
rs1466275	0.92[ASN][1000 genomes]
rs2061197	0.87[JPT][hapmap]
rs2168443	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs2242116	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs2290545	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2290546	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305634	0.81[JPT][hapmap]
rs2305638	0.81[JPT][hapmap]
rs4078466	0.81[JPT][hapmap]
rs4082155	0.81[JPT][hapmap]
rs4539969	0.90[ASN][1000 genomes]
rs4587	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682837	0.87[JPT][hapmap]
rs4682844	0.87[JPT][hapmap];0.86[MEX][hapmap]
rs4682845	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683296	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683297	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683298	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683299	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683300	0.93[ASN][1000 genomes]
rs4683301	0.84[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.89[ASN][1000 genomes]
rs6442038	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6442039	0.89[ASN][1000 genomes]
rs6442040	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6780601	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724448	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs724449	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs724450	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7623898	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7628747	0.87[JPT][hapmap]
rs7635480	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7645278	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7646906	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9852082	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9855938	CCDC12	cis	cerebellum	SCAN
rs9855938	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs9855938	SCAP	cis	cerebellum	SCAN
rs9855938	IMPDH2	cis	parietal	SCAN
rs9855938	SCAP	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46950400-46958800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:46950600-46961800	Weak transcription	Aorta	Aorta
3	chr3:46951000-46957400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:46951000-46959000	Weak transcription	Fetal Brain Female	brain
5	chr3:46951200-46957800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:46951200-46958200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:46951200-46958400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:46951200-46958600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:46951200-46958600	Weak transcription	Brain Germinal Matrix	brain
10	chr3:46951200-46958600	Weak transcription	Fetal Brain Male	brain
11	chr3:46951200-46960400	Weak transcription	Colonic Mucosa	Colon
12	chr3:46951400-46957800	Weak transcription	Primary B cells from cord blood	blood
13	chr3:46951400-46958200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:46951400-46958400	Weak transcription	Fetal Kidney	kidney
15	chr3:46951400-46961600	Weak transcription	Stomach Mucosa	stomach
16	chr3:46951600-46958200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:46951600-46958400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:46951600-46958400	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:46951600-46958600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:46951600-46958600	Weak transcription	Fetal Intestine Large	intestine
21	chr3:46951600-46958800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:46951600-46958800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:46951600-46958800	Weak transcription	Fetal Intestine Small	intestine
24	chr3:46951600-46958800	Weak transcription	NHDF-Ad	bronchial
25	chr3:46951600-46959400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:46951600-46959600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:46951600-46960200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:46951600-46960200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:46951600-46960200	Weak transcription	Brain Substantia Nigra	brain
30	chr3:46951600-46960200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:46951600-46960800	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:46951600-46961800	Weak transcription	HepG2	liver
33	chr3:46951600-46962400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:46951800-46957800	Weak transcription	Fetal Thymus	thymus
35	chr3:46951800-46958600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:46951800-46958600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:46951800-46958600	Weak transcription	K562	blood
38	chr3:46953200-46958600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:46954800-46958400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:46955000-46957400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr3:46955200-46958400	Weak transcription	Dnd41	blood
42	chr3:46955400-46959600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:46955600-46957800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:46955600-46958200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:46955600-46958200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr3:46955600-46958400	Weak transcription	Fetal Lung	lung
47	chr3:46955600-46958600	Weak transcription	Placenta	Placenta
48	chr3:46955600-46958800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:46955600-46958800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:46955600-46958800	Weak transcription	Stomach Smooth Muscle	stomach

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