Variant report

Variant	rs10197738
Chromosome Location	chr2:38921498-38921499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38823862..38826061-chr2:38919360..38922289,2	K562	blood:
2	chr2:38909532..38914838-chr2:38917160..38922190,4	K562	blood:
3	chr2:38914950..38917916-chr2:38919871..38923223,3	K562	blood:
4	chr2:38920104..38923601-chr2:38924114..38926921,3	K562	blood:
5	chr2:38876173..38878521-chr2:38919650..38921533,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10194503	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10206629	0.85[YRI][hapmap]
rs13391054	1.00[ASW][hapmap]
rs17023037	0.96[AFR][1000 genomes]
rs6752602	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7590813	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10197738	GALM	cis	lymphoblastoid	seeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
2	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:38903600-38923800	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:38904800-38936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:38905000-38935800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:38905200-38925400	Weak transcription	Small Intestine	intestine
8	chr2:38909200-38947800	Weak transcription	Right Ventricle	heart
9	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:38909600-38947800	Weak transcription	Brain Anterior Caudate	brain
11	chr2:38909800-38938600	Weak transcription	Fetal Kidney	kidney
12	chr2:38910000-38948000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:38912600-38932000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:38912800-38924200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:38913800-38938800	Weak transcription	Fetal Brain Male	brain
16	chr2:38914400-38930000	Weak transcription	Left Ventricle	heart
17	chr2:38914600-38922800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:38914600-38935600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:38914600-38938600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:38914600-38948000	Weak transcription	Spleen	Spleen
21	chr2:38915800-38947200	Weak transcription	Ovary	ovary
22	chr2:38916600-38932600	Weak transcription	Lung	lung
23	chr2:38916800-38923000	Weak transcription	Adipose Nuclei	Adipose
24	chr2:38916800-38938800	Weak transcription	Fetal Lung	lung
25	chr2:38917000-38921800	Strong transcription	Liver	Liver
26	chr2:38917000-38923600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:38917000-38927800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:38917200-38922800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:38917200-38924600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:38917200-38936400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:38918000-38949400	Weak transcription	Primary B cells from cord blood	blood
32	chr2:38918400-38921600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:38918600-38927400	Strong transcription	Fetal Intestine Small	intestine
34	chr2:38918600-38929600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:38918600-38947600	Weak transcription	Hela-S3	cervix
36	chr2:38918600-38956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:38918800-38923200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr2:38918800-38929600	Weak transcription	HSMM	muscle
39	chr2:38918800-38937200	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:38919200-38921600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr2:38919200-38921800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr2:38919200-38922800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:38919400-38922400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:38919600-38922400	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr2:38919600-38924400	Strong transcription	Fetal Stomach	stomach
46	chr2:38919800-38922200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr2:38919800-38927200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:38920200-38924400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:38920200-38928400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:38920200-38929000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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