Variant report

Variant	rs10279376
Chromosome Location	chr7:7233913-7233914
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7223378..7225133-chr7:7233745..7235333,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1008897	0.80[ASN][1000 genomes]
rs10246303	0.80[ASN][1000 genomes]
rs10246435	0.80[ASN][1000 genomes]
rs10251492	0.80[ASN][1000 genomes]
rs10251505	1.00[ASN][1000 genomes]
rs10253167	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10257662	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10279324	0.80[ASN][1000 genomes]
rs10279432	0.80[ASN][1000 genomes]
rs10281784	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10952045	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12702588	0.86[ASN][1000 genomes]
rs2024122	0.80[ASN][1000 genomes]
rs2108780	0.80[ASN][1000 genomes]
rs2108790	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347893	0.80[ASN][1000 genomes]
rs3807862	0.80[ASN][1000 genomes]
rs4141100	0.80[ASN][1000 genomes]
rs4318980	0.96[ASN][1000 genomes]
rs4720727	0.90[ASN][1000 genomes]
rs5010183	0.80[ASN][1000 genomes]
rs57552003	0.86[ASN][1000 genomes]
rs6463652	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6463656	1.00[ASN][1000 genomes]
rs6463657	1.00[ASN][1000 genomes]
rs767298	0.80[ASN][1000 genomes]
rs7788032	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790219	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs971481	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv508445	chr7:7190518-7261098	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
17	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
18	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10279376	C1GALT1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7223200-7234000	Weak transcription	Small Intestine	intestine
2	chr7:7223400-7240800	Weak transcription	Esophagus	oesophagus
3	chr7:7223400-7241400	Weak transcription	Pancreas	Pancrea
4	chr7:7223800-7234800	Weak transcription	Right Ventricle	heart
5	chr7:7223800-7240800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr7:7223800-7241000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:7223800-7279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:7225000-7243200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr7:7225200-7241000	Weak transcription	HMEC	breast
10	chr7:7225200-7241200	Weak transcription	Hela-S3	cervix
11	chr7:7226000-7240800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:7226200-7235200	Weak transcription	Brain Substantia Nigra	brain
13	chr7:7227400-7241000	Weak transcription	Fetal Thymus	thymus
14	chr7:7228000-7240800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:7228000-7241200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr7:7230000-7234200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:7230000-7240800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:7230000-7241000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr7:7230200-7234800	Weak transcription	Liver	Liver
20	chr7:7230200-7241000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:7230200-7246600	Weak transcription	Osteobl	bone
22	chr7:7230400-7241800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:7230600-7235600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr7:7230600-7241000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:7231200-7235400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr7:7231200-7240000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr7:7231200-7240800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:7231200-7240800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:7231200-7240800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:7231200-7240800	Weak transcription	NHEK	skin
31	chr7:7231400-7241200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:7231400-7248400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr7:7231600-7243000	Weak transcription	HSMM	muscle
34	chr7:7231800-7235000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr7:7232000-7234000	Enhancers	Dnd41	blood
36	chr7:7232200-7235600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr7:7232400-7235600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr7:7232400-7240800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr7:7232600-7235400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr7:7232600-7235600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:7232800-7234000	Weak transcription	HepG2	liver
42	chr7:7232800-7235400	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr7:7233000-7234000	Enhancers	Thymus	Thymus
44	chr7:7233000-7234000	ZNF genes & repeats	GM12878-XiMat	blood
45	chr7:7233200-7234200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr7:7233200-7234200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:7233400-7235600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:7233400-7235600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr7:7233600-7234200	Enhancers	Primary B cells from peripheral blood	blood
50	chr7:7233600-7234200	Enhancers	Sigmoid Colon	Sigmoid Colon

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