Variant report

Variant	rs11575248
Chromosome Location	chr12:56735990-56735991
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56726418..56729508-chr12:56735018..56739337,4	MCF-7	breast:
2	chr12:56723403..56725387-chr12:56735305..56737091,2	MCF-7	breast:
3	chr12:56735954..56738255-chr12:56739970..56742035,3	K562	blood:

Variant related genes	Relation type
ENSG00000135473	Chromatin interaction
ENSG00000170581	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10876882	0.81[EUR][1000 genomes]
rs11171803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575224	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11575229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575234	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274490	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274493	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295772	0.91[ASN][1000 genomes]
rs17118403	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118409	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118431	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17118439	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1802236	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2020854	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066807	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066808	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2066819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306693	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2371454	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2371494	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629447	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643623	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2643626	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695782	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695788	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695789	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35526714	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41392645	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41423244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57343616	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57367440	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57870697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58852079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59295315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59811639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59822547	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59917308	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60542959	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60913149	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs703830	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744051	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs773652	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773664	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773665	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808919	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs871130	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[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
rs11575248	RP11-977G19.11	cis	Artery Tibial	GTEx
rs11575248	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs11575248	RP11-977G19.11	cis	Artery Aorta	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56728400-56736400	Weak transcription	Ovary	ovary
2	chr12:56728400-56736400	Weak transcription	Small Intestine	intestine
3	chr12:56728600-56736400	Weak transcription	Fetal Brain Female	brain
4	chr12:56728600-56736400	Weak transcription	Fetal Kidney	kidney
5	chr12:56728600-56736400	Weak transcription	Gastric	stomach
6	chr12:56728600-56736400	Weak transcription	Pancreas	Pancrea
7	chr12:56728600-56736400	Weak transcription	NHLF	lung
8	chr12:56728600-56736600	Weak transcription	Aorta	Aorta
9	chr12:56728600-56736800	Weak transcription	Colonic Mucosa	Colon
10	chr12:56728600-56739600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:56728600-56748200	Weak transcription	Fetal Brain Male	brain
12	chr12:56728800-56736200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:56728800-56736200	Weak transcription	Psoas Muscle	Psoas
14	chr12:56728800-56736400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:56728800-56736400	Weak transcription	Brain Angular Gyrus	brain
16	chr12:56728800-56736400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:56728800-56736400	Weak transcription	Brain Substantia Nigra	brain
18	chr12:56728800-56736400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:56728800-56736400	Weak transcription	Fetal Lung	lung
20	chr12:56728800-56736400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:56728800-56736400	Weak transcription	Right Ventricle	heart
22	chr12:56728800-56736400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:56728800-56736600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:56728800-56736600	Weak transcription	HUVEC	blood vessel
25	chr12:56728800-56736600	Weak transcription	NHDF-Ad	bronchial
26	chr12:56728800-56736800	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:56728800-56737000	Weak transcription	A549	lung
28	chr12:56728800-56742200	Weak transcription	Stomach Mucosa	stomach
29	chr12:56728800-56752600	Weak transcription	Fetal Heart	heart
30	chr12:56729000-56736400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:56729000-56736400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:56729000-56737000	Weak transcription	Hela-S3	cervix
33	chr12:56732800-56736000	Weak transcription	Brain Germinal Matrix	brain
34	chr12:56733000-56736400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:56733000-56736400	Weak transcription	Dnd41	blood
36	chr12:56733000-56736600	Weak transcription	K562	blood
37	chr12:56733000-56753200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr12:56733200-56736200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:56733200-56736200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr12:56733200-56736400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr12:56733200-56736400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:56733200-56736400	Weak transcription	NH-A	brain
43	chr12:56733200-56736800	Weak transcription	Esophagus	oesophagus
44	chr12:56733400-56736200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:56733400-56736400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr12:56733400-56736400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:56733400-56736400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr12:56733400-56736600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:56733400-56739800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:56733600-56736400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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