Variant report

Variant	rs10225975
Chromosome Location	chr7:7262523-7262524
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	chr7:7261680..7264153-chr7:7267649..7269493,2	K562	blood:
2	chr7:7258238..7260698-chr7:7260877..7262796,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10256877	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10272173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10277583	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10278474	0.93[CEU][hapmap]
rs10447684	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10487590	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11972106	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13222351	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13225339	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13234717	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13238772	0.84[AMR][1000 genomes]
rs13246962	0.85[AMR][1000 genomes]
rs17251749	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34386799	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34419200	0.84[AMR][1000 genomes]
rs34491888	0.84[AMR][1000 genomes]
rs34705126	0.84[AMR][1000 genomes]
rs34971257	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35362940	0.80[EUR][1000 genomes]
rs62449960	0.84[AMR][1000 genomes]
rs62449964	0.84[AMR][1000 genomes]
rs62449965	0.84[AMR][1000 genomes]
rs62450007	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9648103	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10225975	C1GALT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 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	chr7:7241600-7263000	Weak transcription	Right Atrium	heart
3	chr7:7241600-7273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:7247600-7275000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr7:7247800-7267400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:7248600-7263200	Weak transcription	Gastric	stomach
7	chr7:7250800-7296600	Weak transcription	Spleen	Spleen
8	chr7:7252600-7273000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:7253000-7276800	Weak transcription	Fetal Heart	heart
10	chr7:7255000-7266200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:7255400-7267400	Weak transcription	Brain Substantia Nigra	brain
12	chr7:7256200-7267400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:7256200-7270400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:7256600-7263200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr7:7256800-7262800	Weak transcription	Psoas Muscle	Psoas
16	chr7:7256800-7267400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:7256800-7275000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr7:7256800-7297000	Weak transcription	Lung	lung
19	chr7:7257200-7270600	Weak transcription	Liver	Liver
20	chr7:7257200-7274800	Weak transcription	Fetal Thymus	thymus
21	chr7:7257400-7263400	Weak transcription	Fetal Lung	lung
22	chr7:7257400-7263800	Weak transcription	GM12878-XiMat	blood
23	chr7:7257400-7279800	Weak transcription	Fetal Kidney	kidney
24	chr7:7257600-7263400	Weak transcription	Dnd41	blood
25	chr7:7257600-7268600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:7257600-7271400	Weak transcription	Fetal Intestine Small	intestine
27	chr7:7257600-7275200	Weak transcription	Thymus	Thymus
28	chr7:7257600-7298200	Weak transcription	Ovary	ovary
29	chr7:7257600-7299800	Weak transcription	Fetal Stomach	stomach
30	chr7:7257800-7277000	Weak transcription	Fetal Muscle Leg	muscle
31	chr7:7258000-7270600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr7:7258000-7274200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr7:7258000-7276800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr7:7258200-7263000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr7:7258200-7268000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr7:7258200-7274600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr7:7258400-7262800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:7258400-7263600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr7:7258400-7263600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr7:7258400-7264400	Weak transcription	Brain Anterior Caudate	brain
41	chr7:7258400-7264400	Weak transcription	Fetal Brain Female	brain
42	chr7:7258400-7266400	Weak transcription	Primary T cells from cord blood	blood
43	chr7:7258400-7267000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr7:7258400-7267400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr7:7258400-7268800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr7:7258400-7270400	Weak transcription	Fetal Intestine Large	intestine
47	chr7:7258600-7263200	Weak transcription	Primary B cells from cord blood	blood
48	chr7:7258800-7270000	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr7:7258800-7273600	Weak transcription	Placenta	Placenta
50	chr7:7259000-7263400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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