Variant report

Variant	rs738656
Chromosome Location	chr22:31935347-31935348
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	PML	chr22:31934521-31935405	GM12878	blood:	n/a	n/a
2	NFATC1	chr22:31934671-31935427	GM12878	blood:	n/a	n/a
3	RELA	chr22:31934475-31935376	GM18505	blood:	n/a	n/a
4	CREB1	chr22:31934640-31935386	GM12878	blood:	n/a	n/a
5	MTA3	chr22:31934595-31935466	GM12878	blood:	n/a	n/a
6	ATF2	chr22:31934659-31935425	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:31930706-31935473..22:32012966-32043914	GM12878	blood:
2	22:31864703-31891033..22:31930706-31935473	GM12878	blood:

Variant related genes	Relation type
ENSG00000229169	TF binding region
ENSG00000241878	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000199248	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11089512	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11089514	0.85[ASN][1000 genomes]
rs11089515	0.92[ASN][1000 genomes]
rs12170867	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs12171042	1.00[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs12484606	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12627933	0.89[MEX][hapmap]
rs13056823	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs140078	0.84[MEX][hapmap]
rs140081	0.83[MEX][hapmap]
rs1543416	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17821102	0.82[CHB][hapmap]
rs2024747	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2092905	0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs2236033	0.85[JPT][hapmap];0.89[MEX][hapmap]
rs2295242	0.95[JPT][hapmap]
rs2295251	0.95[CEU][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap]
rs2387	0.95[JPT][hapmap]
rs2413053	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3804087	0.84[MEX][hapmap]
rs3818134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535154	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4820051	0.85[JPT][hapmap]
rs4820976	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4820978	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820979	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820980	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820981	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820982	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4820983	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5749280	0.82[CHB][hapmap]
rs5749287	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749293	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs5749297	0.91[ASN][1000 genomes]
rs5749303	0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs5749304	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs5749306	0.81[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap]
rs5753620	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs5753622	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs5753627	0.82[CHB][hapmap]
rs5753633	0.80[CHD][hapmap]
rs5753647	0.83[ASN][1000 genomes]
rs5753650	0.83[ASN][1000 genomes]
rs5753657	0.85[ASN][1000 genomes]
rs5753667	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5753675	0.88[ASN][1000 genomes]
rs5753677	0.92[ASN][1000 genomes]
rs5753680	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753681	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs5753684	0.97[ASN][1000 genomes]
rs5753686	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs5753687	0.85[ASN][1000 genomes]
rs5753690	0.83[ASN][1000 genomes]
rs5753691	0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs5753714	0.85[JPT][hapmap]
rs5753734	1.00[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs59285943	0.88[ASN][1000 genomes]
rs5994415	0.85[JPT][hapmap];0.84[MEX][hapmap]
rs5998011	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5998032	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998035	0.88[EUR][1000 genomes]
rs5998042	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs5998054	0.82[CHD][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap]
rs5998086	0.84[MEX][hapmap]
rs7288464	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7289075	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs7291918	0.95[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs738684	0.80[JPT][hapmap];0.89[MEX][hapmap]
rs738702	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs761746	1.00[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap]
rs8461	0.86[GIH][hapmap];0.94[MEX][hapmap]
rs9306266	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9621269	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9621279	0.81[EUR][1000 genomes]
rs9956	0.95[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]

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	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv1059314	chr22:31893613-31936088	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv914978	chr22:31897795-31942770	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs738656	TCN2	cis	cerebellum	SCAN
rs738656	SFI1	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31893400-31971200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr22:31893600-31946600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr22:31893600-31970000	Weak transcription	Colonic Mucosa	Colon
4	chr22:31893800-31945600	Weak transcription	Brain Anterior Caudate	brain
5	chr22:31894000-31946600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr22:31894000-31946600	Weak transcription	Fetal Brain Female	brain
7	chr22:31900800-31940800	Weak transcription	NHEK	skin
8	chr22:31904400-31944200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr22:31905200-31957200	Weak transcription	A549	lung
10	chr22:31905600-31946200	Weak transcription	Esophagus	oesophagus
11	chr22:31907400-31946400	Weak transcription	Brain Germinal Matrix	brain
12	chr22:31907400-31946600	Weak transcription	Left Ventricle	heart
13	chr22:31907600-31946200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr22:31907800-31942800	Weak transcription	Fetal Intestine Large	intestine
15	chr22:31911800-31946000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr22:31918000-31940600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr22:31921800-31942800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr22:31923000-31945800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr22:31924000-31943600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr22:31925000-31946200	Weak transcription	Adipose Nuclei	Adipose
21	chr22:31925200-31942000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr22:31925600-31942800	Weak transcription	Lung	lung
23	chr22:31925800-31936800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr22:31925800-31936800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr22:31925800-31957200	Weak transcription	Brain Angular Gyrus	brain
26	chr22:31926000-31940800	Weak transcription	Fetal Intestine Small	intestine
27	chr22:31926800-31946200	Weak transcription	Fetal Muscle Leg	muscle
28	chr22:31926800-31950200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr22:31927000-31946200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr22:31927000-31946200	Weak transcription	Liver	Liver
31	chr22:31927000-31946400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr22:31927200-31936800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr22:31927200-31946000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr22:31927200-31946400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr22:31927400-31945600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr22:31927400-31946200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr22:31927400-31946800	Weak transcription	HSMM	muscle
38	chr22:31927400-31961400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr22:31927400-31970000	Weak transcription	NH-A	brain
40	chr22:31927400-31970200	Weak transcription	Fetal Lung	lung
41	chr22:31927400-31979400	Weak transcription	NHDF-Ad	bronchial
42	chr22:31927400-31980000	Weak transcription	HSMMtube	muscle
43	chr22:31927600-31974200	Weak transcription	Small Intestine	intestine
44	chr22:31928200-31948800	Weak transcription	Osteobl	bone
45	chr22:31928400-31939800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr22:31928600-31942200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr22:31928800-31944400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr22:31929000-31936800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr22:31929000-31942800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr22:31929000-31945600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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