Variant report

Variant	rs11575229
Chromosome Location	chr12:56750737-56750738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56732615..56735568-chr12:56748598..56751443,2	K562	blood:
2	chr12:56748050..56751002-chr12:56753460..56756305,2	K562	blood:
3	chr12:56725978..56729877-chr12:56750632..56755261,5	MCF-7	breast:
4	chr12:56747914..56751304-chr12:56752091..56755313,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135473	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000110944	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap]
rs11171803	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11171806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11575231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11575234	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11575248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1274490	0.91[ASN][1000 genomes]
rs1274493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.82[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];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17118409	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[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];0.82[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17118439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1802236	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2020854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2066807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2066808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2066818	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];0.85[ASN][1000 genomes]
rs2066819	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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2306693	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]
rs2306694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2371454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[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];0.82[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2629447	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2643626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2695782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2695788	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2695789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35526714	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41363748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs41392645	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]
rs41423244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57343616	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs57367440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57870697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58852079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59295315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59811639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59822547	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59917308	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60542959	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60913149	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs703830	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs744051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs773652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs773664	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs773665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs808919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[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];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[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
rs11575229	RP11-977G19.11	cis	Artery Tibial	GTEx
rs11575229	RP11-977G19.11	cis	Artery Aorta	GTEx
rs11575229	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	chr12:56728800-56752600	Weak transcription	Fetal Heart	heart
2	chr12:56733000-56753200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:56734000-56750800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:56734800-56750800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:56734800-56750800	Strong transcription	Fetal Muscle Leg	muscle
6	chr12:56735000-56750800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:56735000-56750800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:56735000-56750800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr12:56735000-56750800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr12:56735000-56750800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:56735000-56750800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:56735000-56750800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr12:56735000-56750800	Strong transcription	Fetal Thymus	thymus
14	chr12:56735200-56750800	Strong transcription	Primary T cells from cord blood	blood
15	chr12:56735200-56750800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:56735200-56751400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:56735200-56751800	Strong transcription	Fetal Stomach	stomach
18	chr12:56735800-56750800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:56736000-56750800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr12:56736200-56751800	Strong transcription	Fetal Intestine Small	intestine
21	chr12:56736400-56750800	Strong transcription	Brain Cingulate Gyrus	brain
22	chr12:56739400-56750800	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:56739400-56750800	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:56741600-56750800	Strong transcription	NHDF-Ad	bronchial
25	chr12:56745200-56751200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:56745200-56752600	Weak transcription	Psoas Muscle	Psoas
27	chr12:56747800-56750800	Strong transcription	Brain Germinal Matrix	brain
28	chr12:56747800-56752600	Weak transcription	Right Atrium	heart
29	chr12:56748200-56750800	Strong transcription	HSMM	muscle
30	chr12:56748800-56751400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:56749400-56750800	Genic enhancers	Liver	Liver
32	chr12:56749400-56753400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:56749600-56752800	Weak transcription	Stomach Mucosa	stomach
34	chr12:56749800-56752200	Weak transcription	HMEC	breast
35	chr12:56749800-56752400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr12:56750000-56751200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:56750000-56751600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:56750000-56752400	Weak transcription	HUVEC	blood vessel
39	chr12:56750000-56752400	Weak transcription	K562	blood
40	chr12:56750000-56752600	Weak transcription	Fetal Brain Male	brain
41	chr12:56750000-56753000	Weak transcription	Small Intestine	intestine
42	chr12:56750200-56751600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr12:56750200-56751800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr12:56750200-56751800	Weak transcription	Brain Angular Gyrus	brain
45	chr12:56750200-56751800	Weak transcription	Fetal Lung	lung
46	chr12:56750200-56752000	Weak transcription	Colonic Mucosa	Colon
47	chr12:56750200-56752200	Weak transcription	Colon Smooth Muscle	Colon
48	chr12:56750200-56752400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:56750200-56752400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:56750200-56752400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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