Variant report

Variant	rs41392645
Chromosome Location	chr12:56696742-56696743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:56696720-56696870	AG10803	skin:	n/a	n/a
2	CTCF	chr12:56696740-56696890	A549	lung:	n/a	n/a
3	CTCF	chr12:56696700-56696850	HRE	kidney:	n/a	n/a
4	CTCF	chr12:56696680-56696830	HCM	heart:	n/a	n/a
5	CTCF	chr12:56695763-56696742	SK-N-SH	brain:	n/a	chr12:56696321-56696337 chr12:56696315-56696336 chr12:56696320-56696338 chr12:56696326-56696335 chr12:56696322-56696335
6	CTCF	chr12:56696680-56696830	HVMF	connective:	n/a	n/a
7	CTCF	chr12:56696660-56696810	GM12864	blood:	n/a	n/a
8	PAX5	chr12:56696439-56696755	GM12878	blood:	n/a	n/a
9	CTCF	chr12:56695635-56696796	A549	lung:	n/a	chr12:56696321-56696337 chr12:56696315-56696336 chr12:56696320-56696338 chr12:56696326-56696335 chr12:56696322-56696335
10	CTCF	chr12:56696700-56696850	WI-38	lung:	n/a	n/a
11	ZNF384	chr12:56696186-56696790	GM12878	blood:	n/a	n/a
12	CTCF	chr12:56696600-56696750	AoAF	blood vessel:	n/a	n/a
13	PAX5	chr12:56696331-56696774	GM12878	blood:	n/a	n/a
14	CTCF	chr12:56696660-56696810	HMF	breast:	n/a	n/a
15	CTCF	chr12:56696680-56696830	Caco-2	colon:	n/a	n/a
16	CTCF	chr12:56696700-56696850	GM12864	blood:	n/a	n/a
17	CTCF	chr12:56696680-56696830	GM12875	blood:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56692256..56696973-chr12:56707335..56712231,9	K562	blood:
2	chr12:56586878..56587381-chr12:56696043..56696785,2	K562	blood:
3	chr12:56690986..56698275-chr12:56706607..56711958,20	MCF-7	breast:
4	chr12:56652045..56652731-chr12:56695880..56696766,2	MCF-7	breast:
5	chr12:56690402..56700610-chr12:56705161..56712229,20	K562	blood:
6	chr12:56693116..56697525-chr12:56726716..56730598,5	K562	blood:
7	chr12:56695752..56697519-chr12:56726820..56729640,2	MCF-7	breast:
8	chr12:56617925..56618696-chr12:56695888..56696814,2	K562	blood:
9	chr12:56679574..56682384-chr12:56692383..56696875,5	K562	blood:
10	chr12:56694767..56697892-chr12:56702654..56704783,4	K562	blood:
11	chr12:56509513..56513531-chr12:56694540..56697702,5	K562	blood:
12	chr12:56694994..56697860-chr12:56698216..56699984,2	MCF-7	breast:
13	chr12:56693640..56697163-chr12:56700934..56704368,3	MCF-7	breast:
14	chr12:56679574..56681804-chr12:56694461..56697113,2	K562	blood:
15	chr12:56509293..56514359-chr12:56692717..56696999,9	K562	blood:
16	chr12:56585782..56587966-chr12:56695653..56698357,2	K562	blood:
17	chr12:56625939..56627578-chr12:56694733..56696853,2	K562	blood:
18	chr12:56696025..56697572-chr12:56726476..56728778,2	K562	blood:
19	chr12:56696417..56698207-chr12:56857084..56858822,2	MCF-7	breast:

No data

Variant related genes	Relation type
CS	TF binding region
ENSG00000135482	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000257740	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000062485	Chromatin interaction

Extended variants
information (count: 60 )
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];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];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];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575231	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575232	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	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];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17118409	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];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	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[AFR][1000 genomes];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];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];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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306693	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]
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];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];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]
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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57137641	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57279772	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57343616	0.82[AMR][1000 genomes]
rs57367440	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57870697	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58852079	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59295315	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59626664	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59811639	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	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	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];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];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3409718	chr12:56696427-56696939	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41392645	RP11-977G19.11	cis	Artery Tibial	GTEx
rs41392645	RP11-977G19.11	cis	Artery Aorta	GTEx
rs41392645	TMEM4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56694600-56704400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56694600-56708400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56694800-56696800	Enhancers	Primary T cells fromperipheralblood	blood
4	chr12:56694800-56697200	Enhancers	Primary B cells from peripheral blood	blood
5	chr12:56694800-56697600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:56694800-56708200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:56694800-56708800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:56695000-56696800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr12:56695000-56697000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr12:56695000-56697200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:56695000-56697200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:56695000-56697200	Weak transcription	Fetal Brain Female	brain
13	chr12:56695000-56697800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:56695000-56698000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:56695000-56698200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:56695000-56698600	Weak transcription	Brain Angular Gyrus	brain
17	chr12:56695000-56699000	Weak transcription	NH-A	brain
18	chr12:56695000-56700400	Weak transcription	Brain Germinal Matrix	brain
19	chr12:56695000-56700400	Weak transcription	Thymus	Thymus
20	chr12:56695000-56701800	Weak transcription	Ovary	ovary
21	chr12:56695000-56702000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:56695000-56702800	Weak transcription	Small Intestine	intestine
23	chr12:56695000-56703600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:56695000-56703600	Weak transcription	Esophagus	oesophagus
25	chr12:56695000-56703600	Weak transcription	Gastric	stomach
26	chr12:56695000-56704600	Weak transcription	Aorta	Aorta
27	chr12:56695000-56708000	Weak transcription	Fetal Brain Male	brain
28	chr12:56695000-56708600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:56695200-56697000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:56695200-56697000	Weak transcription	Fetal Lung	lung
31	chr12:56695200-56697800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr12:56695200-56697800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:56695200-56697800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:56695200-56697800	Enhancers	Liver	Liver
35	chr12:56695200-56697800	Weak transcription	Placenta	Placenta
36	chr12:56695200-56697800	Weak transcription	Osteobl	bone
37	chr12:56695200-56698000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr12:56695200-56698000	Weak transcription	NHEK	skin
39	chr12:56695200-56698200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr12:56695200-56698200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:56695200-56698200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:56695200-56698200	Weak transcription	NHLF	lung
43	chr12:56695200-56698400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:56695200-56698600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:56695200-56698600	Weak transcription	Adipose Nuclei	Adipose
46	chr12:56695200-56698800	Weak transcription	Fetal Kidney	kidney
47	chr12:56695200-56699800	Weak transcription	Lung	lung
48	chr12:56695200-56700400	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:56695200-56701800	Weak transcription	HSMMtube	muscle
50	chr12:56695200-56702000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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