Variant report

Variant	rs7373072
Chromosome Location	chr3:48960017-48960018
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48752504..48754863-chr3:48957920..48960085,2	K562	blood:

Variant related genes	Relation type
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 17 )

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

rs_ID	r²[population]
rs11130181	0.81[EUR][1000 genomes]
rs11707968	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12715430	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13099075	0.85[EUR][1000 genomes]
rs14018	1.00[CEU][hapmap]
rs3087866	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs3212	0.81[YRI][hapmap]
rs4292260	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs4955411	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs4955416	1.00[CEU][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs4955426	0.95[CEU][hapmap]
rs4974079	0.88[YRI][hapmap]
rs4974080	0.81[YRI][hapmap]
rs4974081	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4974083	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4974087	0.88[YRI][hapmap]
rs4974088	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs62259536	0.91[EUR][1000 genomes]
rs6414614	0.85[EUR][1000 genomes]
rs6442130	0.88[YRI][hapmap]
rs6446196	0.81[YRI][hapmap]
rs6446200	0.93[EUR][1000 genomes]
rs6446204	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6446205	0.85[YRI][hapmap]
rs6446247	0.83[EUR][1000 genomes]
rs6446252	0.89[YRI][hapmap]
rs6446253	0.81[YRI][hapmap]
rs6766238	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6772452	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6779394	0.88[YRI][hapmap]
rs6787808	1.00[CEU][hapmap]
rs6796790	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs6798112	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6801211	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs7100	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs7372883	0.90[EUR][1000 genomes]
rs7430198	0.85[YRI][hapmap]
rs7432989	0.88[YRI][hapmap]
rs7434187	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7627404	0.88[YRI][hapmap]
rs7639370	0.82[EUR][1000 genomes]
rs7653408	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes]
rs9311431	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9637481	0.93[YRI][hapmap]
rs9682444	0.88[YRI][hapmap]
rs9755490	0.88[YRI][hapmap]
rs9810318	0.84[EUR][1000 genomes]
rs9835307	0.88[YRI][hapmap]
rs9840050	0.81[YRI][hapmap]
rs9850134	0.82[YRI][hapmap]
rs9859473	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9864243	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9876848	0.88[YRI][hapmap]
rs9879978	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9884022	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv980012	chr3:48935037-48963512	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv3394753	chr3:48956248-48960046	Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv3340246	chr3:48956448-48960646	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	esv3461083	chr3:48956973-48960121	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7373072	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs7373072	AMT	cis	Adipose Subcutaneous	GTEx
rs7373072	WDR6	cis	Muscle Skeletal	GTEx
rs7373072	NICN1-AS1	cis	Thyroid	GTEx
rs7373072	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs7373072	WDR6	cis	Heart Left Ventricle	GTEx
rs7373072	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs7373072	WDR6	cis	Nerve Tibial	GTEx
rs7373072	WDR6	cis	lung	GTEx
rs7373072	AMT	cis	lung	GTEx
rs7373072	AMT	cis	Artery Tibial	GTEx
rs7373072	NCKIPSD	cis	Nerve Tibial	GTEx
rs7373072	AMT	cis	Nerve Tibial	GTEx
rs7373072	AMT	cis	Whole Blood	GTEx
rs7373072	QRICH1	cis	Nerve Tibial	GTEx
rs7373072	NICN1	cis	Thyroid	GTEx
rs7373072	AMT	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48957200-48965000	Weak transcription	Small Intestine	intestine
2	chr3:48957400-48961400	Weak transcription	Ovary	ovary
3	chr3:48957400-49003800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:48957600-48961400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:48957600-48961400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:48957600-48964400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:48957600-48964400	Weak transcription	HSMMtube	muscle
8	chr3:48957600-48965000	Weak transcription	Fetal Kidney	kidney
9	chr3:48957600-48974400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:48957800-48961000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:48957800-48961000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:48957800-48961200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:48957800-48961200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:48957800-48961200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:48957800-48961200	Weak transcription	Colonic Mucosa	Colon
16	chr3:48957800-48961200	Weak transcription	NH-A	brain
17	chr3:48957800-48961400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:48957800-48961400	Weak transcription	NHEK	skin
19	chr3:48957800-48961600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:48957800-48963000	Weak transcription	NHDF-Ad	bronchial
21	chr3:48957800-48963400	Weak transcription	HSMM	muscle
22	chr3:48957800-48964000	Weak transcription	HMEC	breast
23	chr3:48957800-48964600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:48957800-48964600	Weak transcription	Aorta	Aorta
25	chr3:48957800-48965000	Weak transcription	Right Ventricle	heart
26	chr3:48958000-48963600	Weak transcription	A549	lung
27	chr3:48958000-48964400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:48958000-48964400	Weak transcription	Stomach Mucosa	stomach
29	chr3:48958000-48965000	Weak transcription	Fetal Brain Male	brain
30	chr3:48958400-48964000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:48958800-48965400	Strong transcription	Fetal Intestine Small	intestine
32	chr3:48959000-48960600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:48959000-48965200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:48959000-48965200	Strong transcription	Fetal Stomach	stomach
35	chr3:48959000-48968400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:48959000-48971600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:48959000-48974000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:48959000-48976000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:48959000-48976200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:48959200-48962200	Strong transcription	Fetal Lung	lung
41	chr3:48959200-48962800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:48959200-48963800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:48959200-48964000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:48959200-48964200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:48959200-48964800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:48959200-48965000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr3:48959200-48968200	Strong transcription	Thymus	Thymus
48	chr3:48959200-48971000	Strong transcription	Fetal Muscle Leg	muscle
49	chr3:48959200-48973600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:48959400-48960200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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