Variant report

Variant	rs40942
Chromosome Location	chr7:108203050-108203051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108175296..108178679-chr7:108201125..108203447,3	K562	blood:
2	chr7:108168430..108172542-chr7:108200740..108204398,3	K562	blood:
3	chr7:108202468..108204754-chr7:108208486..108210281,2	MCF-7	breast:
4	chr7:108191362..108206184-chr7:108206645..108216261,27	K562	blood:
5	chr7:108200654..108204288-chr7:108205009..108207830,4	MCF-7	breast:
6	chr7:108159403..108171484-chr7:108200740..108214365,45	K562	blood:
7	chr7:108165059..108167985-chr7:108201651..108203639,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128590	Chromatin interaction
ENSG00000135241	Chromatin interaction
ENSG00000177683	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12666562	0.87[EUR][1000 genomes]
rs35372181	0.90[EUR][1000 genomes]
rs3763457	0.87[EUR][1000 genomes]
rs40912	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40914	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40915	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40919	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40921	0.83[EUR][1000 genomes]
rs40923	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40924	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40925	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40928	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40931	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40932	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40934	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs40936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40938	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40939	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40940	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40941	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40944	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40945	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40946	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40947	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40948	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs40942	THAP5	cis	normal skin	skin_eQTL
rs40942	THAP5	cis	uninvolved skin	skin_eQTL
rs40942	THAP5	cis	multi-tissue	Pritchard
rs40942	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108191400-108204600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:108195600-108208400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:108197600-108208600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:108197800-108208600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:108198000-108204200	Weak transcription	Fetal Thymus	thymus
6	chr7:108198000-108208400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:108198400-108207800	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:108198400-108208400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:108198600-108204200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:108198600-108204200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr7:108198600-108204600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:108198600-108204800	Weak transcription	Dnd41	blood
13	chr7:108198600-108207400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:108198600-108208600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr7:108198600-108208600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:108198600-108208600	Weak transcription	Fetal Brain Male	brain
17	chr7:108198600-108208600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:108198600-108208600	Weak transcription	Thymus	Thymus
19	chr7:108198800-108204200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:108198800-108204200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:108198800-108204400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr7:108198800-108204400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr7:108198800-108205800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:108198800-108206000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr7:108199000-108207600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:108199400-108207400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr7:108199400-108208200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr7:108199600-108204200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:108199600-108204600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:108199600-108204600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:108199800-108204200	Weak transcription	K562	blood
32	chr7:108199800-108204800	Weak transcription	Adipose Nuclei	Adipose
33	chr7:108199800-108204800	Weak transcription	GM12878-XiMat	blood
34	chr7:108200000-108204000	Weak transcription	Fetal Lung	lung
35	chr7:108200000-108204200	Weak transcription	Liver	Liver
36	chr7:108200000-108207000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr7:108200000-108207800	Weak transcription	HepG2	liver
38	chr7:108200200-108204600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:108200200-108206000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr7:108200200-108208000	Weak transcription	Brain Angular Gyrus	brain
41	chr7:108200400-108209400	Weak transcription	Spleen	Spleen
42	chr7:108200600-108208400	Weak transcription	NHLF	lung
43	chr7:108201200-108208600	Weak transcription	Pancreas	Pancrea
44	chr7:108201400-108204200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr7:108201600-108204200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr7:108201600-108204800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr7:108201600-108207200	Weak transcription	HUVEC	blood vessel
48	chr7:108201600-108208600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr7:108201600-108208600	Weak transcription	Left Ventricle	heart
50	chr7:108201600-108208600	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links