Variant report

Variant	rs2572003
Chromosome Location	chr7:99501313-99501314
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99500402..99502716-chr7:99515554..99517966,2	MCF-7	breast:
2	chr7:99493888..99497270-chr7:99498893..99502551,4	K562	blood:
3	chr7:99461799..99464694-chr7:99500550..99502670,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146833	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1025576	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1048705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10808114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1121592	0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12535919	1.00[YRI][hapmap]
rs12536945	1.00[YRI][hapmap]
rs13310903	0.84[ASN][1000 genomes]
rs1865472	0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2060452	0.96[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2082744	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2082745	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2099445	0.80[ASN][1000 genomes]
rs2247761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247762	0.82[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2525541	0.85[CHB][hapmap]
rs2525542	0.81[EUR][1000 genomes]
rs2525548	0.85[CHB][hapmap]
rs2527886	0.84[CHB][hapmap]
rs2527890	0.84[CHB][hapmap]
rs2527894	0.84[CHB][hapmap]
rs2527897	0.84[CHB][hapmap]
rs2527899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527900	0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527902	0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527904	0.96[ASN][1000 genomes]
rs2527906	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2527908	0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2527909	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527911	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527912	0.97[ASN][1000 genomes]
rs2527913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527916	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2527918	0.88[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2527919	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527920	0.97[ASN][1000 genomes]
rs2527921	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527925	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2527926	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527927	0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2571991	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2571992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571993	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571994	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571995	0.96[ASN][1000 genomes]
rs2571996	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571999	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2572000	0.88[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2572002	0.92[ASN][1000 genomes]
rs2572005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2572006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2572008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572009	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572010	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572011	0.96[ASN][1000 genomes]
rs2572012	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2572013	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2572015	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2572018	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2572019	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2572022	0.92[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2572023	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs2572024	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4727439	0.97[ASN][1000 genomes]
rs474229	0.92[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs503115	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7781442	0.88[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7809747	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2572003	TRIM4	cis	lung	GTEx
rs2572003	TRIM4	cis	multi-tissue	Pritchard
rs2572003	TRIM4	cis	Artery Tibial	GTEx
rs2572003	TRIM4	cis	Nerve Tibial	GTEx
rs2572003	TRIM4	cis	Thyroid	GTEx
rs2572003	TRIM4	cis	Esophagus Muscularis	GTEx
rs2572003	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2572003	TRIM4	cis	Esophagus Mucosa	GTEx
rs2572003	TRIM4	cis	Whole Blood	GTEx
rs2572003	TRIM4	cis	Skin Sun Exposed Lower leg	GTEx
rs2572003	TRIM4	cis	Muscle Skeletal	GTEx
rs2572003	TRIM4	cis	lesional skin	skin_eQTL
rs2572003	TRIM4	cis	Stomach	GTEx
rs2572003	TRIM4	cis	Artery Aorta	GTEx
rs2572003	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2572003	TRIM4	cis	uninvolved skin	skin_eQTL
rs2572003	TRIM4	cis	Lymphoblastoid	GTEx
rs2572003	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs2572003	TRIM4	cis	normal skin	skin_eQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99492600-99516600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:99494600-99508800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:99494800-99507200	Strong transcription	Stomach Smooth Muscle	stomach
4	chr7:99495400-99501600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:99495400-99501600	Strong transcription	Lung	lung
6	chr7:99495400-99501800	Strong transcription	Primary B cells from cord blood	blood
7	chr7:99495400-99504800	Strong transcription	Fetal Brain Female	brain
8	chr7:99495400-99507200	Strong transcription	Brain Inferior Temporal Lobe	brain
9	chr7:99495400-99510200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:99495400-99514400	Weak transcription	Stomach Mucosa	stomach
11	chr7:99495600-99501800	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr7:99495600-99504800	Strong transcription	Brain Germinal Matrix	brain
13	chr7:99495600-99507200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:99495600-99507200	Strong transcription	Brain Angular Gyrus	brain
15	chr7:99495600-99507400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:99495600-99507400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:99495600-99507400	Strong transcription	Adipose Nuclei	Adipose
18	chr7:99495600-99507400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr7:99495600-99507600	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr7:99495600-99507600	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:99495600-99509600	Strong transcription	Primary T cells from cord blood	blood
22	chr7:99495600-99510200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr7:99495600-99510800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:99495800-99501600	Strong transcription	Brain Cingulate Gyrus	brain
25	chr7:99495800-99504800	Strong transcription	NHLF	lung
26	chr7:99495800-99507200	Strong transcription	Brain Hippocampus Middle	brain
27	chr7:99495800-99507200	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr7:99495800-99507200	Strong transcription	Left Ventricle	heart
29	chr7:99495800-99507600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr7:99495800-99507800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:99495800-99508000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr7:99495800-99508200	Strong transcription	A549	lung
33	chr7:99495800-99510000	Strong transcription	Fetal Thymus	thymus
34	chr7:99495800-99510200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:99495800-99510600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr7:99496000-99504200	Strong transcription	Brain Anterior Caudate	brain
37	chr7:99496000-99507400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:99496000-99507400	Strong transcription	Fetal Intestine Large	intestine
39	chr7:99496000-99507600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr7:99496000-99509600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr7:99496200-99509400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:99496400-99504600	Strong transcription	Fetal Muscle Leg	muscle
43	chr7:99496400-99505800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr7:99496400-99507200	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:99496400-99507400	Strong transcription	Liver	Liver
46	chr7:99496400-99508800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr7:99496400-99510000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr7:99496400-99510600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:99496600-99501600	Strong transcription	Fetal Lung	lung
50	chr7:99496600-99507200	Strong transcription	Muscle Satellite Cultured Cells	--

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