Variant report

Variant	rs40948
Chromosome Location	chr7:108208802-108208803
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:108208427-108208962	Hela-S3	cervix:	n/a	n/a
2	JUN	chr7:108208251-108211889	K562	blood:	n/a	n/a
3	BHLHE40	chr7:108208641-108211651	K562	blood:	n/a	chr7:108209635-108209648
4	POLR2A	chr7:108208569-108209035	K562	blood:	n/a	n/a
5	POLR2A	chr7:108199426-108221976	K562	blood:	n/a	n/a
6	ZNF384	chr7:108208330-108209032	K562	blood:	n/a	n/a
7	POLR2A	chr7:108208528-108211292	K562	blood:	n/a	n/a
8	UBTF	chr7:108208611-108208870	K562	blood:	n/a	n/a
9	IRF1	chr7:108208152-108210573	K562	blood:	n/a	chr7:108209590-108209602 chr7:108208528-108208541 chr7:108208531-108208542 chr7:108208530-108208544
10	MAX	chr7:108208636-108208864	K562	blood:	n/a	n/a
11	POLR2A	chr7:108208545-108208888	MCF-7	breast:	n/a	n/a
12	MXI1	chr7:108207302-108212533	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr7:108208325-108211370	K562	blood:	n/a	n/a
14	POLR2A	chr7:108208446-108211787	MCF10A-Er-Src	breast:	n/a	n/a
15	JUND	chr7:108208408-108208968	K562	blood:	n/a	n/a
16	TCF7L2	chr7:108208482-108208962	PANC-1	pancreas:	n/a	n/a
17	TBL1XR1	chr7:108208759-108208820	K562	blood:	n/a	n/a
18	MAX	chr7:108208564-108208946	K562	blood:	n/a	n/a
19	MYC	chr7:108208454-108208961	K562	blood:	n/a	n/a
20	MAX	chr7:108208607-108208836	K562	blood:	n/a	n/a
21	E2F6	chr7:108208687-108208864	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:108164038..108167949-chr7:108208349..108211666,8	MCF-7	breast:
2	chr7:107383523..107385849-chr7:108208781..108210517,2	K562	blood:
3	chr7:108163122..108173185-chr7:108207236..108216619,40	K562	blood:
4	chr7:108159403..108171484-chr7:108200740..108214365,45	K562	blood:
5	chr7:108208069..108211100-chr7:112089167..112092388,3	K562	blood:
6	chr7:108162967..108170259-chr7:108208242..108216228,25	MCF-7	breast:

No data

Variant related genes	Relation type
DNAJB9	TF binding region
ENSG00000135241	Chromatin interaction
ENSG00000105879	Chromatin interaction
ENSG00000006652	Chromatin interaction
ENSG00000241764	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40914	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40915	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40919	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40921	0.82[EUR][1000 genomes]
rs40923	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs40924	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs40925	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs40926	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40928	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs40931	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40932	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40934	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs40936	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40938	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40939	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40940	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40941	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs40942	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40944	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40945	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40946	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40947	0.85[AMR][1000 genomes];0.91[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs40948	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108200400-108209400	Weak transcription	Spleen	Spleen
2	chr7:108202200-108209200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:108205200-108209400	Weak transcription	Gastric	stomach
4	chr7:108205400-108209200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:108206400-108209200	Weak transcription	Aorta	Aorta
6	chr7:108206400-108209200	Weak transcription	Fetal Muscle Leg	muscle
7	chr7:108206400-108209200	Weak transcription	Ovary	ovary
8	chr7:108206600-108209000	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr7:108206800-108209000	Weak transcription	Fetal Kidney	kidney
10	chr7:108207000-108209200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:108207000-108209200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr7:108207200-108209000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr7:108207200-108209200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr7:108207200-108209200	Enhancers	Fetal Heart	heart
15	chr7:108207400-108213400	Active TSS	GM12878-XiMat	blood
16	chr7:108207600-108212000	Active TSS	K562	blood
17	chr7:108207800-108209000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:108207800-108209000	Enhancers	Brain Hippocampus Middle	brain
19	chr7:108207800-108209600	Flanking Active TSS	Dnd41	blood
20	chr7:108208000-108209000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr7:108208000-108209000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:108208000-108209000	Enhancers	Brain Angular Gyrus	brain
23	chr7:108208000-108209000	Enhancers	Fetal Brain Female	brain
24	chr7:108208200-108209000	Enhancers	Primary T cells from cord blood	blood
25	chr7:108208200-108209000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:108208200-108209200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:108208200-108209600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr7:108208400-108209000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:108208400-108209000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:108208400-108209000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr7:108208400-108209000	Flanking Active TSS	Liver	Liver
32	chr7:108208400-108209000	Enhancers	NH-A	brain
33	chr7:108208400-108209000	Enhancers	Osteobl	bone
34	chr7:108208400-108209200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr7:108208400-108209200	Enhancers	Primary B cells from peripheral blood	blood
36	chr7:108208400-108209200	Enhancers	Primary hematopoietic stem cells	blood
37	chr7:108208400-108209200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:108208400-108209200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr7:108208400-108209200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr7:108208400-108209200	Enhancers	Fetal Intestine Small	intestine
41	chr7:108208400-108209200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr7:108208400-108209200	Enhancers	Rectal Smooth Muscle	rectum
43	chr7:108208400-108209200	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr7:108208400-108209400	Enhancers	Small Intestine	intestine
45	chr7:108208400-108209400	Enhancers	Stomach Mucosa	stomach
46	chr7:108208400-108209600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:108208400-108209600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr7:108208400-108209600	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr7:108208400-108209600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr7:108208400-108209600	Flanking Active TSS	Hela-S3	cervix

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