Variant report

Variant	rs2306693
Chromosome Location	chr12:56680531-56680532
allele	C/T
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	chr12:56680217-56680946	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:56680423-56680929	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:56680485-56680613	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:56680297-56680923	HepG2	liver:	n/a	n/a
5	RAD21	chr12:56680517-56680983	SK-N-SH	brain:	n/a	chr12:56680836-56680848 chr12:56680836-56680846

No.	Distal block	Cell Line	Cell type
1	chr12:56614513..56617977-chr12:56679402..56681953,3	K562	blood:
2	chr12:56673715..56677406-chr12:56679436..56684365,5	K562	blood:
3	chr12:56679574..56682384-chr12:56692383..56696875,5	K562	blood:
4	chr12:56661026..56663843-chr12:56677963..56681395,3	K562	blood:
5	chr12:56679574..56681804-chr12:56694461..56697113,2	K562	blood:
6	chr12:56510082..56512448-chr12:56678488..56681005,3	MCF-7	breast:

Variant related genes	Relation type
CS	TF binding region
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000062485	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10876882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11171803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575224	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11575229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575231	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575234	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575248	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274490	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295772	0.91[ASN][1000 genomes]
rs17118403	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17118409	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17118439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1802236	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2020854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2066819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2371454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2371494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629447	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643623	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2643626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695788	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35526714	0.83[EUR][1000 genomes]
rs41363748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap]
rs41392645	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41423244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57343616	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs57367440	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57870697	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58852079	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59295315	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59811639	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59822547	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59917308	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60542959	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60913149	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs703830	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs773652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773664	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[ASN][1000 genomes]
rs871130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2306693	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2306693	RP11-977G19.11	cis	Artery Aorta	GTEx
rs2306693	RP11-977G19.11	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56661400-56684400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:56662000-56690000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:56662400-56680800	Strong transcription	Brain Hippocampus Middle	brain
4	chr12:56662400-56692400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:56662600-56680800	Strong transcription	Placenta	Placenta
6	chr12:56662600-56681000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr12:56662600-56681000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:56662600-56681400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:56662600-56682800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:56662600-56685400	Strong transcription	Fetal Thymus	thymus
11	chr12:56662600-56686000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:56662600-56690000	Strong transcription	Fetal Muscle Leg	muscle
13	chr12:56662800-56680600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:56662800-56680800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:56662800-56680800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:56662800-56680800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:56662800-56680800	Strong transcription	Thymus	Thymus
18	chr12:56662800-56681000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:56662800-56681000	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:56662800-56682000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:56662800-56682200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:56662800-56682800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr12:56662800-56683200	Strong transcription	Dnd41	blood
24	chr12:56662800-56686400	Strong transcription	Fetal Stomach	stomach
25	chr12:56663000-56680600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:56663000-56680600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:56663000-56692600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:56663200-56680800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr12:56663200-56685600	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:56663400-56682200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:56663400-56687000	Strong transcription	Fetal Intestine Small	intestine
32	chr12:56663600-56680600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:56663600-56680800	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:56663600-56684600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:56663800-56680600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:56663800-56680600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr12:56663800-56680800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:56663800-56684400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:56663800-56685600	Strong transcription	Fetal Intestine Large	intestine
40	chr12:56663800-56685800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr12:56664000-56681200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr12:56664000-56682600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:56664200-56680800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr12:56664400-56680800	Strong transcription	Brain Germinal Matrix	brain
45	chr12:56664800-56682800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:56666000-56680800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:56667000-56681000	Strong transcription	GM12878-XiMat	blood
48	chr12:56667400-56685400	Weak transcription	Fetal Heart	heart
49	chr12:56667800-56685400	Weak transcription	Stomach Mucosa	stomach
50	chr12:56669600-56692800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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