Variant report

Variant	rs10487590
Chromosome Location	chr7:7277263-7277264
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	chr7:7273518..7275790-chr7:7276170..7278082,2	MCF-7	breast:
2	chr7:7276448..7278083-chr7:7286333..7288584,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MIOS-5	chr7:7277049-7277531	l_3358_chr7:7273087-7284245_placenta

Variant related genes	Relation type
ENSG00000106392	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10225975	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10256877	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10272173	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10277583	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11972106	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13222351	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13225339	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13234717	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13246962	0.81[AMR][1000 genomes]
rs13438509	1.00[CHD][hapmap]
rs17251749	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17252812	0.81[AMR][1000 genomes]
rs2116533	1.00[CHD][hapmap]
rs2163639	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs34386799	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35362940	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4582461	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs62450007	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62450018	0.82[AMR][1000 genomes]
rs6976254	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1023133	chr7:6854098-7516700	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	nsv464300	chr7:7040176-7368699	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv606033	chr7:7040176-7368699	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv1016369	chr7:7053923-7375567	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv1023788	chr7:7053923-7407783	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv538720	chr7:7053923-7407783	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
10	nsv1032813	chr7:7053923-7497484	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
13	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription 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 miRNA target site	54 gene(s)	inside rSNPs	diseases
14	nsv1032974	chr7:7145831-7393218	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
16	esv2758102	chr7:7209911-7493901	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	esv2759505	chr7:7209911-7493901	Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
18	nsv464301	chr7:7252775-7442169	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
19	nsv606035	chr7:7252775-7442169	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
20	nsv469770	chr7:7261414-7453821	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
21	nsv433018	chr7:7269171-7348778	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
22	nsv606036	chr7:7273559-7343909	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10487590	C1GALT1	Cis_1M	lymphoblastoid	RTeQTL
rs10487590	C1GALT1	cis	parietal	SCAN
rs10487590	ZHX2	trans	lymphoblastoid	seeQTL
rs10487590	C1GALT1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7223800-7279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:7250800-7296600	Weak transcription	Spleen	Spleen
3	chr7:7256800-7297000	Weak transcription	Lung	lung
4	chr7:7257400-7279800	Weak transcription	Fetal Kidney	kidney
5	chr7:7257600-7298200	Weak transcription	Ovary	ovary
6	chr7:7257600-7299800	Weak transcription	Fetal Stomach	stomach
7	chr7:7260400-7297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:7261600-7277800	Weak transcription	A549	lung
9	chr7:7261600-7296800	Weak transcription	Aorta	Aorta
10	chr7:7261600-7298000	Weak transcription	Pancreas	Pancrea
11	chr7:7261600-7299400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:7261800-7278800	Weak transcription	Left Ventricle	heart
13	chr7:7262000-7278400	Weak transcription	NH-A	brain
14	chr7:7262200-7286600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:7265200-7278400	Weak transcription	Fetal Brain Female	brain
16	chr7:7265400-7287200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr7:7271400-7298200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:7271600-7287000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr7:7271800-7286000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:7271800-7289000	Weak transcription	Fetal Intestine Small	intestine
21	chr7:7272400-7295000	Weak transcription	Small Intestine	intestine
22	chr7:7272400-7296600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:7272800-7278400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
24	chr7:7273000-7278800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr7:7273000-7280000	Strong transcription	HepG2	liver
26	chr7:7273000-7280200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:7273000-7280400	Strong transcription	Primary B cells from cord blood	blood
28	chr7:7273000-7287000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr7:7273200-7280000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:7273200-7291200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr7:7273400-7281800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr7:7273400-7311200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr7:7273600-7280200	Strong transcription	Primary T cells from cord blood	blood
34	chr7:7273600-7280400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:7273600-7280600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr7:7273600-7281000	Strong transcription	Osteobl	bone
37	chr7:7273600-7285600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr7:7273600-7286400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr7:7273800-7279200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr7:7273800-7279400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr7:7273800-7280600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr7:7273800-7285000	Weak transcription	HUVEC	blood vessel
43	chr7:7274000-7280000	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr7:7274000-7280000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr7:7274000-7280800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr7:7274000-7281200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr7:7274400-7284000	Strong transcription	HSMM	muscle
48	chr7:7274600-7280000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr7:7274600-7301600	Weak transcription	Brain Germinal Matrix	brain
50	chr7:7274800-7280400	Strong transcription	Fetal Thymus	thymus

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