Variant report

Variant	rs11575234
Chromosome Location	chr12:56744276-56744277
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56740489..56742180-chr12:56743721..56745673,2	MCF-7	breast:
2	chr12:56739323..56741090-chr12:56743159..56745608,2	K562	blood:
3	chr12:56727294..56730824-chr12:56743728..56746098,3	MCF-7	breast:
4	chr12:56726854..56730634-chr12:56743613..56745998,4	K562	blood:
5	chr12:56743017..56746738-chr12:56752337..56755444,3	K562	blood:

Variant related genes	Relation type
ENSG00000135473	Chromatin interaction
ENSG00000170581	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10876882	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11171803	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171806	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171812	0.96[AFR][1000 genomes]
rs11575221	0.92[AFR][1000 genomes]
rs11575224	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11575229	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11575231	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575232	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575236	0.98[AFR][1000 genomes]
rs11575248	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274490	0.82[ASN][1000 genomes]
rs1274493	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1295772	0.82[ASN][1000 genomes]
rs17118403	0.82[ASN][1000 genomes]
rs17118409	0.82[ASN][1000 genomes]
rs17118439	0.81[EUR][1000 genomes]
rs1802236	0.81[ASN][1000 genomes]
rs1918496	0.87[AFR][1000 genomes]
rs2020854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066807	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2066808	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2066818	0.94[EUR][1000 genomes]
rs2066819	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291361	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306693	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306694	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2371454	0.82[ASN][1000 genomes]
rs2371494	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2629447	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2643623	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2643626	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695782	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695788	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695789	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41392645	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41423244	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57137641	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57279772	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57367440	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57870697	0.94[EUR][1000 genomes]
rs58852079	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59295315	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59626664	0.82[ASN][1000 genomes]
rs59811639	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59822547	0.82[ASN][1000 genomes]
rs59917308	0.81[EUR][1000 genomes]
rs60192809	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60913149	0.82[ASN][1000 genomes]
rs703830	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73324336	0.91[AFR][1000 genomes]
rs744051	0.81[EUR][1000 genomes]
rs773652	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773664	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773665	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs808919	0.82[ASN][1000 genomes]
rs871130	0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11575234	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs11575234	RP11-977G19.11	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56728600-56748200	Weak transcription	Fetal Brain Male	brain
2	chr12:56728800-56752600	Weak transcription	Fetal Heart	heart
3	chr12:56733000-56753200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:56733600-56747000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:56734000-56750800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr12:56734800-56750600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:56734800-56750800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:56734800-56750800	Strong transcription	Fetal Muscle Leg	muscle
9	chr12:56735000-56746800	Strong transcription	HSMM	muscle
10	chr12:56735000-56750200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:56735000-56750400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:56735000-56750400	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:56735000-56750400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:56735000-56750400	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr12:56735000-56750400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:56735000-56750400	Strong transcription	Adipose Nuclei	Adipose
17	chr12:56735000-56750400	Strong transcription	Brain Hippocampus Middle	brain
18	chr12:56735000-56750800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:56735000-56750800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:56735000-56750800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr12:56735000-56750800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr12:56735000-56750800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:56735000-56750800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:56735000-56750800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:56735000-56750800	Strong transcription	Fetal Thymus	thymus
26	chr12:56735200-56749400	Strong transcription	Liver	Liver
27	chr12:56735200-56750200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:56735200-56750400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:56735200-56750400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:56735200-56750400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:56735200-56750400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:56735200-56750400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:56735200-56750400	Strong transcription	Brain Anterior Caudate	brain
34	chr12:56735200-56750400	Strong transcription	Placenta	Placenta
35	chr12:56735200-56750600	Strong transcription	Primary B cells from cord blood	blood
36	chr12:56735200-56750800	Strong transcription	Primary T cells from cord blood	blood
37	chr12:56735200-56750800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:56735200-56751400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:56735200-56751800	Strong transcription	Fetal Stomach	stomach
40	chr12:56735400-56744600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:56735800-56750400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:56735800-56750400	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:56735800-56750800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:56736000-56750400	Strong transcription	Fetal Intestine Large	intestine
45	chr12:56736000-56750800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr12:56736200-56750200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:56736200-56750400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr12:56736200-56751800	Strong transcription	Fetal Intestine Small	intestine
49	chr12:56736400-56745800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr12:56736400-56746800	Strong transcription	Fetal Brain Female	brain

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