Variant report

Variant	rs71325388
Chromosome Location	chr3:119354257-119354258
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119326194..119327898-chr3:119353631..119355784,2	K562	blood:
2	chr3:119297207..119300144-chr3:119352679..119354693,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272967	Chromatin interaction
ENSG00000144843	Chromatin interaction
ENSG00000144837	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11914676	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11923223	0.87[ASN][1000 genomes]
rs12487499	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488460	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490779	0.99[ASN][1000 genomes]
rs12492456	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1403631	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1525836	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16830115	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830291	0.87[ASN][1000 genomes]
rs17203235	0.99[ASN][1000 genomes]
rs1797827	0.92[ASN][1000 genomes]
rs1872432	0.87[ASN][1000 genomes]
rs1985121	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280578	0.87[ASN][1000 genomes]
rs2670292	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688629	0.92[ASN][1000 genomes]
rs2688630	0.92[ASN][1000 genomes]
rs2688631	0.92[ASN][1000 genomes]
rs2688634	0.97[ASN][1000 genomes]
rs2692616	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2698283	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34097211	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34593263	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34787881	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35043554	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35256565	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4234662	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4629367	0.87[ASN][1000 genomes]
rs4687869	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688021	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688024	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs524043	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs525916	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs540420	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs572119	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs575833	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs579196	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67683909	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6783324	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6789941	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6790938	0.91[ASN][1000 genomes]
rs6792417	0.87[ASN][1000 genomes]
rs6803814	0.87[ASN][1000 genomes]
rs68150601	0.86[ASN][1000 genomes]
rs71325389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7613825	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8422	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876919	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3463490	chr3:119350258-119354322	Enhancers Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1796433	chr3:119350324-119360506	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv591371	chr3:119351398-119354433	Enhancers Weak transcription Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1804126	chr3:119351398-119360506	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv591374	chr3:119351650-119354433	Enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv591384	chr3:119352069-119354433	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv963354	chr3:119352662-119355854	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv527724	chr3:119353844-119361415	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs71325388	RP11-190C22.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119340800-119357600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:119341400-119364600	Weak transcription	Liver	Liver
3	chr3:119345200-119357600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:119345800-119355200	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:119347800-119356400	Weak transcription	Fetal Thymus	thymus
6	chr3:119349400-119357600	Weak transcription	Fetal Intestine Small	intestine
7	chr3:119349600-119354400	Weak transcription	Fetal Stomach	stomach
8	chr3:119349600-119355000	Weak transcription	Spleen	Spleen
9	chr3:119349600-119357000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:119349800-119354400	Weak transcription	Right Atrium	heart
11	chr3:119349800-119355000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:119349800-119356400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:119349800-119356400	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:119349800-119357000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:119349800-119378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:119350000-119354400	Weak transcription	Lung	lung
17	chr3:119350000-119354600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:119350000-119354600	Weak transcription	GM12878-XiMat	blood
19	chr3:119350000-119354600	Weak transcription	HUVEC	blood vessel
20	chr3:119350000-119354800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:119350000-119354800	Weak transcription	NHDF-Ad	bronchial
22	chr3:119350000-119355000	Weak transcription	NH-A	brain
23	chr3:119350000-119355000	Weak transcription	NHLF	lung
24	chr3:119350000-119355200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:119350400-119354800	Weak transcription	HSMM	muscle
26	chr3:119350400-119355000	Weak transcription	HSMMtube	muscle
27	chr3:119350600-119354800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:119350600-119355000	Weak transcription	Osteobl	bone
29	chr3:119351000-119354800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:119351000-119355000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:119351000-119355000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:119351200-119354800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:119351400-119354600	Weak transcription	Pancreas	Pancrea
34	chr3:119351400-119354600	Weak transcription	Psoas Muscle	Psoas
35	chr3:119351400-119354800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:119351400-119355000	Weak transcription	K562	blood
37	chr3:119351400-119355400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:119351600-119354400	Weak transcription	Adipose Nuclei	Adipose
39	chr3:119351600-119355200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:119351800-119356400	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:119352000-119354400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:119352000-119354600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:119352000-119355000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:119352000-119355000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr3:119352000-119357400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:119352000-119378600	Weak transcription	Thymus	Thymus
47	chr3:119352600-119354400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:119352600-119367000	Weak transcription	Ovary	ovary
49	chr3:119352800-119356600	Weak transcription	Aorta	Aorta
50	chr3:119353800-119359000	Strong transcription	Stomach Smooth Muscle	stomach

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