Variant report

Variant	rs4767938
Chromosome Location	chr12:121261162-121261163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121261119..121262624-chr12:121287692..121289232,2	MCF-7	breast:
2	chr12:121259584..121261305-chr12:121284288..121286336,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1105416	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11065286	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1151851	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1168945	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1168954	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1168956	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1696363	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1718211	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2454729	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2649996	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2649998	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2650006	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs3844037	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs482522	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs487310	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs487912	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs493811	0.96[ASN][1000 genomes]
rs497273	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs498230	0.94[ASN][1000 genomes]
rs520405	0.96[ASN][1000 genomes]
rs532140	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs532703	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs550349	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs551087	0.90[JPT][hapmap]
rs564120	0.93[ASN][1000 genomes]
rs566994	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs584001	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs586305	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs589699	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs594507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs597203	0.93[ASN][1000 genomes]
rs610578	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs619679	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs633084	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6553	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs656933	0.81[ASN][1000 genomes]
rs662284	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs662739	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs674021	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs679833	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs680303	0.96[ASN][1000 genomes]
rs683091	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs683437	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs688402	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs694303	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs791210	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs791707	0.94[ASN][1000 genomes]

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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1045178	chr12:121231461-121271734	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4767938	WSB2	cis	cerebellum	SCAN
rs4767938	UNC119B	cis	cerebellum	SCAN
rs4767938	SPPL3	cis	cerebellum	SCAN
rs4767938	SPPL3	cis	parietal	SCAN
rs4767938	P2RX4	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121222200-121274000	Weak transcription	Lung	lung
2	chr12:121222600-121268600	Weak transcription	Esophagus	oesophagus
3	chr12:121222600-121268600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr12:121234000-121264200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:121234600-121263000	Weak transcription	A549	lung
6	chr12:121241000-121261200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:121244800-121264000	Weak transcription	Aorta	Aorta
8	chr12:121248000-121264400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:121248000-121265200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:121248200-121267200	Weak transcription	Fetal Stomach	stomach
11	chr12:121248200-121272200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:121248400-121266800	Weak transcription	Fetal Intestine Large	intestine
13	chr12:121248600-121267200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:121248800-121268600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:121248800-121270400	Weak transcription	Primary B cells from cord blood	blood
16	chr12:121248800-121271600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr12:121248800-121271800	Weak transcription	Dnd41	blood
18	chr12:121250800-121266600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr12:121253800-121268600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:121254000-121268600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:121255200-121261600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:121255800-121270000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:121256000-121261200	Weak transcription	Adipose Nuclei	Adipose
24	chr12:121256000-121266200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:121256000-121267200	Weak transcription	Placenta	Placenta
26	chr12:121257000-121261600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:121258000-121261200	Weak transcription	Fetal Intestine Small	intestine
28	chr12:121259000-121261200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr12:121259000-121261200	Enhancers	Brain Angular Gyrus	brain
30	chr12:121259000-121261600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr12:121259000-121261600	Enhancers	Brain Anterior Caudate	brain
32	chr12:121259000-121261600	Enhancers	Brain Cingulate Gyrus	brain
33	chr12:121259000-121261600	Enhancers	Brain Hippocampus Middle	brain
34	chr12:121259000-121261600	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr12:121259200-121261600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:121259200-121263600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:121259600-121261600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr12:121259600-121262600	Weak transcription	Colon Smooth Muscle	Colon
39	chr12:121259600-121265400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr12:121259800-121261600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:121259800-121261600	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr12:121259800-121261600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr12:121259800-121264800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr12:121260000-121261200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:121260200-121261200	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr12:121260200-121261400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr12:121260200-121268800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr12:121260400-121261400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:121260400-121261600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:121260400-121261600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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