Variant report

Variant	rs40936
Chromosome Location	chr7:108200002-108200003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108166812..108168537-chr7:108199226..108200784,2	MCF-7	breast:
2	chr7:108190740..108192459-chr7:108199194..108201083,2	MCF-7	breast:
3	chr7:108193337..108196664-chr7:108198034..108202692,4	K562	blood:
4	chr7:108191362..108206184-chr7:108206645..108216261,27	K562	blood:

Variant related genes	Relation type
ENSG00000177683	Chromatin interaction
ENSG00000135241	Chromatin interaction
ENSG00000128590	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	0.86[EUR][1000 genomes]
rs35372181	0.91[EUR][1000 genomes]
rs3763457	0.86[EUR][1000 genomes]
rs40912	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40914	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40915	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40919	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40921	0.84[EUR][1000 genomes]
rs40923	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40924	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40925	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40928	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40931	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40932	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40934	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40938	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40939	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40940	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40941	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs40942	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]
rs40944	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40945	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs40946	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40947	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40948	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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
rs40936	THAP5	cis	normal skin	skin_eQTL
rs40936	THAP5	cis	lymphoblastoid	seeQTL
rs40936	THAP5	cis	uninvolved skin	skin_eQTL
rs40936	THAP5	cis	multi-tissue	Pritchard

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108190200-108201400	Weak transcription	HSMMtube	muscle
2	chr7:108191400-108204600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:108195600-108208400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:108197600-108208600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:108197800-108208600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:108198000-108201200	Weak transcription	Placenta	Placenta
7	chr7:108198000-108201600	Weak transcription	HSMM	muscle
8	chr7:108198000-108204200	Weak transcription	Fetal Thymus	thymus
9	chr7:108198000-108208400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:108198400-108207800	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:108198400-108208400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:108198600-108200800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:108198600-108200800	Weak transcription	Ovary	ovary
14	chr7:108198600-108202000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:108198600-108202000	Weak transcription	Primary B cells from cord blood	blood
16	chr7:108198600-108202000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr7:108198600-108203000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr7:108198600-108204200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:108198600-108204200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr7:108198600-108204600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr7:108198600-108204800	Weak transcription	Dnd41	blood
22	chr7:108198600-108207400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:108198600-108208600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr7:108198600-108208600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:108198600-108208600	Weak transcription	Fetal Brain Male	brain
26	chr7:108198600-108208600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:108198600-108208600	Weak transcription	Thymus	Thymus
28	chr7:108198800-108201800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:108198800-108202400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr7:108198800-108204200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:108198800-108204200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:108198800-108204400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr7:108198800-108204400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr7:108198800-108205800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:108198800-108206000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr7:108199000-108202200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr7:108199000-108207600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr7:108199200-108202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:108199400-108202200	Strong transcription	A549	lung
40	chr7:108199400-108207400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr7:108199400-108208200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr7:108199600-108201600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:108199600-108204200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:108199600-108204600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:108199600-108204600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:108199800-108201600	Weak transcription	Fetal Intestine Large	intestine
47	chr7:108199800-108204200	Weak transcription	K562	blood
48	chr7:108199800-108204800	Weak transcription	Adipose Nuclei	Adipose
49	chr7:108199800-108204800	Weak transcription	GM12878-XiMat	blood
50	chr7:108200000-108204000	Weak transcription	Fetal Lung	lung

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