Variant report

Variant	rs17118409
Chromosome Location	chr12:56630764-56630765
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56625950..56631814-chr12:56649549..56655223,8	MCF-7	breast:
2	chr12:56622689..56625267-chr12:56629999..56633597,3	MCF-7	breast:
3	chr12:56510354..56511965-chr12:56629667..56631737,2	K562	blood:

Variant related genes	Relation type
ENSG00000139540	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10876882	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11171803	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171806	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575224	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575229	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]
rs11575231	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11575234	0.82[ASN][1000 genomes]
rs11575248	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274490	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274493	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274496	0.82[EUR][1000 genomes]
rs1295772	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118431	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118439	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1802236	1.00[AFR][1000 genomes]
rs2020854	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2066807	0.89[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]
rs2066808	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2066818	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2066819	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291361	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306693	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]
rs2306694	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2371454	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2371494	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2629447	0.89[CEU][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2629452	0.88[EUR][1000 genomes]
rs2643623	0.84[ASN][1000 genomes]
rs2643626	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695782	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695788	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2695789	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35526714	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41363748	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs41392645	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]
rs41423244	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57343616	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57367440	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57870697	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58852079	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59295315	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59811639	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59822547	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59917308	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60542959	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60913149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703830	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs744051	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773652	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773664	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773665	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs808919	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871130	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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
rs17118409	RP11-977G19.11	cis	Artery Aorta	GTEx
rs17118409	RP11-977G19.11	cis	Artery Tibial	GTEx
rs17118409	TMEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56618600-56633800	Weak transcription	Aorta	Aorta
2	chr12:56618800-56631200	Weak transcription	HSMMtube	muscle
3	chr12:56618800-56633000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:56618800-56633000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:56618800-56634600	Weak transcription	Psoas Muscle	Psoas
6	chr12:56618800-56635200	Weak transcription	Small Intestine	intestine
7	chr12:56618800-56635400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:56618800-56637800	Weak transcription	Fetal Kidney	kidney
9	chr12:56619000-56631000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:56619000-56632000	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:56619000-56633000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:56619000-56633200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:56619000-56633400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:56619000-56633600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr12:56619000-56634000	Weak transcription	Primary B cells from cord blood	blood
16	chr12:56619000-56634800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:56619200-56631000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:56619200-56631200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:56619200-56631400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:56619200-56632400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:56619200-56633000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:56619200-56633000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:56619200-56633000	Weak transcription	Left Ventricle	heart
24	chr12:56619200-56633400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:56619200-56633400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:56619200-56634400	Weak transcription	Fetal Lung	lung
27	chr12:56619200-56634600	Weak transcription	HUVEC	blood vessel
28	chr12:56619200-56635000	Weak transcription	HSMM	muscle
29	chr12:56619200-56635400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr12:56619200-56637600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:56619400-56632600	Weak transcription	NHDF-Ad	bronchial
32	chr12:56619400-56634600	Weak transcription	NH-A	brain
33	chr12:56619400-56637200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:56619400-56637800	Weak transcription	Right Atrium	heart
35	chr12:56619600-56632600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:56619600-56634600	Weak transcription	HMEC	breast
37	chr12:56619600-56635600	Weak transcription	GM12878-XiMat	blood
38	chr12:56619600-56638000	Weak transcription	Hela-S3	cervix
39	chr12:56619800-56638800	Weak transcription	Fetal Brain Male	brain
40	chr12:56620200-56631800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:56620200-56633800	Weak transcription	Brain Substantia Nigra	brain
42	chr12:56621600-56632200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:56621600-56633000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:56621600-56633000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:56623200-56632600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:56623200-56632800	Weak transcription	NHEK	skin
47	chr12:56623200-56633200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr12:56623800-56630800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:56624400-56646000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:56625200-56638400	Weak transcription	Stomach Mucosa	stomach

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