Variant report

Variant	rs40943
Chromosome Location	chr7:108204479-108204480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108202468..108204754-chr7:108208486..108210281,2	MCF-7	breast:
2	chr7:108191362..108206184-chr7:108206645..108216261,27	K562	blood:
3	chr7:108159403..108171484-chr7:108200740..108214365,45	K562	blood:

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

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10156002	0.86[CEU][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10253210	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10270723	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10282368	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1043615	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17426315	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041003	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2072212	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34668718	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40911	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40913	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40916	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40918	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs40922	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40927	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40929	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40930	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40933	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40937	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730324	0.90[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv970570	chr7:108204432-108205276	Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs40943	THAP5	cis	lymphoblastoid	seeQTL
rs40943	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs40943	RINT1	cis	cerebellum	SCAN
rs40943	THAP5	cis	cerebellum	SCAN
rs40943	C7orf66	cis	cerebellum	SCAN
rs40943	DNAJB9	cis	parietal	SCAN

Chromatin state (count:99 , 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	chr7:108198000-108208400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:108198400-108207800	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:108198400-108208400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:108198600-108204600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr7:108198600-108204800	Weak transcription	Dnd41	blood
10	chr7:108198600-108207400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:108198600-108208600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:108198600-108208600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:108198600-108208600	Weak transcription	Fetal Brain Male	brain
14	chr7:108198600-108208600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:108198600-108208600	Weak transcription	Thymus	Thymus
16	chr7:108198800-108205800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:108198800-108206000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr7:108199000-108207600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr7:108199400-108207400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr7:108199400-108208200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:108199600-108204600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:108199600-108204600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:108199800-108204800	Weak transcription	Adipose Nuclei	Adipose
24	chr7:108199800-108204800	Weak transcription	GM12878-XiMat	blood
25	chr7:108200000-108207000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr7:108200000-108207800	Weak transcription	HepG2	liver
27	chr7:108200200-108204600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr7:108200200-108206000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:108200200-108208000	Weak transcription	Brain Angular Gyrus	brain
30	chr7:108200400-108209400	Weak transcription	Spleen	Spleen
31	chr7:108200600-108208400	Weak transcription	NHLF	lung
32	chr7:108201200-108208600	Weak transcription	Pancreas	Pancrea
33	chr7:108201600-108204800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr7:108201600-108207200	Weak transcription	HUVEC	blood vessel
35	chr7:108201600-108208600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:108201600-108208600	Weak transcription	Left Ventricle	heart
37	chr7:108201600-108208600	Weak transcription	Right Ventricle	heart
38	chr7:108201800-108207400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr7:108201800-108208400	Weak transcription	Brain Germinal Matrix	brain
40	chr7:108202000-108207000	Strong transcription	Primary B cells from cord blood	blood
41	chr7:108202000-108207600	Weak transcription	Hela-S3	cervix
42	chr7:108202000-108207800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:108202000-108208400	Weak transcription	Fetal Intestine Small	intestine
44	chr7:108202200-108205200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:108202200-108205200	Weak transcription	Osteobl	bone
46	chr7:108202200-108206200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:108202200-108207200	Weak transcription	Fetal Heart	heart
48	chr7:108202200-108207600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr7:108202200-108208600	Weak transcription	Fetal Stomach	stomach
50	chr7:108202200-108209200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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