Variant report

Variant	rs62449960
Chromosome Location	chr7:7226058-7226059
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:7134412..7137246-chr7:7225961..7227712,2	K562	blood:
2	chr7:7220778..7225200-chr7:7225255..7228969,6	MCF-7	breast:
3	chr7:7216761..7219425-chr7:7225133..7226670,2	K562	blood:
4	chr7:7215938..7217878-chr7:7224426..7227305,2	K562	blood:

Variant related genes	Relation type
ENSG00000244167	Chromatin interaction
ENSG00000106392	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10225975	0.84[AMR][1000 genomes]
rs10256877	0.82[AMR][1000 genomes]
rs10272173	0.84[AMR][1000 genomes]
rs10277583	0.80[AMR][1000 genomes]
rs10447684	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13222351	0.87[AMR][1000 genomes]
rs13234717	0.87[AMR][1000 genomes]
rs13238772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13246962	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17164011	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17249770	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17250084	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17251749	0.87[AMR][1000 genomes]
rs17309555	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2116533	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2116534	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2116535	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2163638	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2163639	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34386799	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34419200	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34491888	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34705126	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34971257	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35362940	0.80[AMR][1000 genomes]
rs4324853	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4428582	0.86[EUR][1000 genomes]
rs4582461	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58312319	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58843310	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62449964	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62449965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62450007	0.82[AMR][1000 genomes]
rs62453491	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62453504	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62453505	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62453506	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62453507	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62453510	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62453511	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62453512	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62453513	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9648103	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv1020929	chr7:6954959-7232920	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats 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	39 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
rs62449960	C1GALT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

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	chr7:7223800-7226400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:7223800-7226600	Enhancers	Fetal Brain Male	brain
6	chr7:7223800-7226800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr7:7223800-7226800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr7:7223800-7227800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:7223800-7228000	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr7:7223800-7228000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr7:7223800-7229600	Weak transcription	NHLF	lung
12	chr7:7223800-7229800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr7:7223800-7230000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:7223800-7234800	Weak transcription	Right Ventricle	heart
15	chr7:7223800-7240800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr7:7223800-7241000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:7223800-7279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:7224000-7226600	Enhancers	Fetal Intestine Small	intestine
19	chr7:7224000-7227600	Weak transcription	Placenta	Placenta
20	chr7:7224000-7228000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr7:7224000-7229600	Weak transcription	Fetal Lung	lung
22	chr7:7224000-7230000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr7:7224000-7230400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr7:7224200-7229400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:7224400-7229600	Weak transcription	A549	lung
26	chr7:7224400-7230000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr7:7224600-7232800	Weak transcription	HUVEC	blood vessel
28	chr7:7224800-7226200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
29	chr7:7224800-7226800	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr7:7225000-7226200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:7225000-7226200	Genic enhancers	HSMM	muscle
32	chr7:7225000-7226400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:7225000-7226400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:7225000-7226600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:7225000-7231000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:7225000-7243200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr7:7225200-7226200	Genic enhancers	H1 Cell Line	embryonic stem cell
38	chr7:7225200-7226600	Enhancers	Brain Hippocampus Middle	brain
39	chr7:7225200-7226600	Enhancers	Dnd41	blood
40	chr7:7225200-7226800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:7225200-7227200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr7:7225200-7227200	Strong transcription	Fetal Thymus	thymus
43	chr7:7225200-7227600	Genic enhancers	Primary T cells from cord blood	blood
44	chr7:7225200-7229200	Weak transcription	NHDF-Ad	bronchial
45	chr7:7225200-7229600	Weak transcription	NH-A	brain
46	chr7:7225200-7233000	Weak transcription	Thymus	Thymus
47	chr7:7225200-7233200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr7:7225200-7241000	Weak transcription	HMEC	breast
49	chr7:7225200-7241200	Weak transcription	Hela-S3	cervix
50	chr7:7225400-7226400	Strong transcription	Primary hematopoietic stem cells	blood

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