Variant report

Variant	rs12419692
Chromosome Location	chr11:47624714-47624715
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47612835..47615053-chr11:47623359..47624985,2	MCF-7	breast:
2	chr11:47614172..47616934-chr11:47623061..47626012,2	K562	blood:
3	chr11:47619408..47621652-chr11:47621906..47625534,3	MCF-7	breast:
4	chr11:47617914..47620881-chr11:47623187..47625181,2	K562	blood:
5	chr11:47600323..47602054-chr11:47624527..47627482,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM180B-2	chr11:47624358-47624726	NONHSAT021264

No data

Variant related genes	Relation type
ENSG00000123444	Chromatin interaction
ENSG00000213619	Chromatin interaction
ENSG00000172247	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1064608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10742803	0.87[CEU][hapmap]
rs10838708	0.90[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10838738	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10838748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10838757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.83[ASN][1000 genomes]
rs11039307	0.86[ASN][1000 genomes]
rs11039308	1.00[ASN][1000 genomes]
rs11039324	0.88[ASN][1000 genomes]
rs11039342	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11039348	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11039355	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11602339	0.80[ASN][1000 genomes]
rs11602395	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11604680	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11604825	0.82[ASN][1000 genomes]
rs11605348	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12361031	0.80[ASN][1000 genomes]
rs12363232	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12419507	0.89[ASN][1000 genomes]
rs12421210	0.82[ASN][1000 genomes]
rs12787112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12787646	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12794570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12798028	0.87[ASN][1000 genomes]
rs12798346	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12799623	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12803191	0.82[ASN][1000 genomes]
rs1317149	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs17788930	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2030166	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2053979	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2290850	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs2293577	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs2293578	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs2868459	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs34910028	0.83[ASN][1000 genomes]
rs34923397	0.81[ASN][1000 genomes]
rs34958982	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs35624992	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3781625	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3781626	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs3781627	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3817334	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs3817335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4752856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752999	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs56400411	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59360790	0.92[ASN][1000 genomes]
rs66749409	0.88[ASN][1000 genomes]
rs7105282	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7124681	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs755553	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs755554	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7927771	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs7928842	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7937331	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs7945473	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7947730	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs9909	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]

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	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs12419692	C1QTNF4	cis	lymphoblastoid	seeQTL
rs12419692	C1QTNF4	cis	multi-tissue	Pritchard
rs12419692	PSMC3	cis	cerebellum	SCAN
rs12419692	MYBPC3	cis	multi-tissue	Pritchard
rs12419692	SLC35C1	cis	parietal	SCAN
rs12419692	C1QTNF4	cis	Artery Tibial	GTEx
rs12419692	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs12419692	ACP2	cis	lymphoblastoid	seeQTL
rs12419692	C1QTNF4	cis	Whole Blood	GTEx
rs12419692	Hs.6637	cis	multi-tissue	Pritchard
rs12419692	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs12419692	MADD	cis	cerebellum	SCAN
rs12419692	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs12419692	C1QTNF4	cis	Muscle Skeletal	GTEx
rs12419692	SPI1	cis	lymphoblastoid	seeQTL
rs12419692	SPI1	cis	multi-tissue	Pritchard
rs12419692	MTCH2	cis	cerebellum	SCAN
rs12419692	C1QTNF4	cis	lung	GTEx
rs12419692	NR1H3	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47607000-47632800	Weak transcription	Dnd41	blood
2	chr11:47616000-47628200	Weak transcription	Right Atrium	heart
3	chr11:47616400-47627000	Weak transcription	Pancreas	Pancrea
4	chr11:47616400-47628200	Weak transcription	HSMMtube	muscle
5	chr11:47616400-47628400	Weak transcription	Ovary	ovary
6	chr11:47616600-47631400	Weak transcription	Spleen	Spleen
7	chr11:47616600-47632400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:47616600-47632600	Weak transcription	Brain Substantia Nigra	brain
9	chr11:47617400-47628200	Weak transcription	Right Ventricle	heart
10	chr11:47617600-47643200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:47617800-47632400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr11:47618000-47628200	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:47618000-47639200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:47618400-47628200	Weak transcription	Fetal Intestine Small	intestine
15	chr11:47618400-47628600	Weak transcription	Liver	Liver
16	chr11:47619200-47627000	Weak transcription	Primary T cells from cord blood	blood
17	chr11:47619400-47631400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:47619600-47631400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr11:47619600-47631600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr11:47620600-47628200	Weak transcription	Thymus	Thymus
21	chr11:47620800-47637800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr11:47621000-47640400	Weak transcription	Fetal Brain Female	brain
23	chr11:47621200-47628800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:47621400-47628200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr11:47621600-47628400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:47621600-47628400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:47621600-47632400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:47621600-47638200	Weak transcription	Hela-S3	cervix
29	chr11:47621600-47647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:47621800-47627600	Weak transcription	NHDF-Ad	bronchial
31	chr11:47621800-47628200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:47621800-47628600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr11:47621800-47629400	Weak transcription	Brain Anterior Caudate	brain
34	chr11:47621800-47631400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:47621800-47632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:47621800-47642000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:47622000-47628200	Weak transcription	Adipose Nuclei	Adipose
38	chr11:47622000-47636000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr11:47622000-47637600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:47623000-47632800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:47623400-47627600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr11:47623800-47624800	Enhancers	HepG2	liver
43	chr11:47623800-47632400	Weak transcription	Gastric	stomach
44	chr11:47624000-47625200	Enhancers	NHLF	lung
45	chr11:47624200-47628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:47624200-47631400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr11:47624200-47632600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr11:47624400-47632400	Weak transcription	Fetal Thymus	thymus
49	chr11:47624600-47624800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:47624600-47624800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

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