Variant report

Variant	rs3843540
Chromosome Location	chr7:99126640-99126641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99124531..99126737-chr7:99155243..99157215,2	K562	blood:
2	chr7:99122366..99125169-chr7:99126048..99128824,3	K562	blood:
3	chr7:99125754..99128092-chr7:99141340..99143007,2	K562	blood:

Variant related genes	Relation type
ENSG00000197343	Chromatin interaction
ENSG00000221909	Chromatin interaction
ENSG00000272647	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1011024	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10155966	0.83[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs10225314	0.87[JPT][hapmap]
rs10231948	0.81[YRI][hapmap]
rs10238965	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10243678	0.83[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs10244158	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10253937	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10254729	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10258757	0.83[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs10265385	0.81[ASN][1000 genomes]
rs10270459	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs10270917	0.83[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs10271049	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10271582	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10272998	0.83[CEU][hapmap]
rs1043466	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11762273	0.83[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs11772470	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap]
rs11976018	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227795	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13240600	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13437771	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1980307	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072181	0.83[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs2240384	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2240385	0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap]
rs2272168	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2280600	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280601	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286162	0.83[CEU][hapmap]
rs2687086	0.84[JPT][hapmap]
rs2740561	0.81[JPT][hapmap]
rs28457808	0.84[ASN][1000 genomes]
rs3137	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34777615	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3779354	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3800960	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801288	0.83[CEU][hapmap]
rs3901286	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45540134	0.82[ASN][1000 genomes]
rs58222677	0.81[ASN][1000 genomes]
rs60301933	0.84[ASN][1000 genomes]
rs61159815	0.82[ASN][1000 genomes]
rs61402640	0.86[ASN][1000 genomes]
rs61543997	0.86[ASN][1000 genomes]
rs6943920	0.83[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap]
rs6961634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs6962772	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7794682	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7794705	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7804551	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868564	0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs883403	0.92[CEU][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917154	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs940334	0.88[YRI][hapmap]
rs940336	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs952319	0.83[CEU][hapmap];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3843540	ACTL6B	cis	cerebellum	SCAN
rs3843540	CPSF4	cis	parietal	SCAN
rs3843540	GATS	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99105000-99128000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:99105000-99128000	Weak transcription	Fetal Heart	heart
3	chr7:99105000-99128800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:99105000-99129400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:99112400-99127400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr7:99113200-99127800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:99118000-99128200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr7:99119400-99126800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:99120000-99127400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:99120800-99127200	Strong transcription	Osteobl	bone
11	chr7:99121400-99127200	Strong transcription	NHDF-Ad	bronchial
12	chr7:99121800-99128400	Strong transcription	Brain Anterior Caudate	brain
13	chr7:99122400-99127400	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr7:99122400-99127400	Strong transcription	Stomach Smooth Muscle	stomach
15	chr7:99122400-99132800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:99122800-99126800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr7:99122800-99127400	Strong transcription	Primary T cells from cord blood	blood
18	chr7:99122800-99127400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:99123000-99126800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:99123000-99126800	Strong transcription	Fetal Intestine Large	intestine
21	chr7:99123000-99127800	Strong transcription	Fetal Brain Female	brain
22	chr7:99123000-99128000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:99123200-99127200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:99123200-99128800	Strong transcription	Brain Angular Gyrus	brain
25	chr7:99123600-99129200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr7:99124000-99128200	Weak transcription	Small Intestine	intestine
27	chr7:99124200-99128000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr7:99124600-99127600	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr7:99124600-99128800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr7:99125000-99131400	ZNF genes & repeats	GM12878-XiMat	blood
31	chr7:99125200-99128000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr7:99125200-99128200	Weak transcription	HepG2	liver
33	chr7:99125200-99131800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr7:99125400-99131800	ZNF genes & repeats	Liver	Liver
35	chr7:99125600-99127200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:99125600-99131800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:99125600-99131800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr7:99125800-99126800	ZNF genes & repeats	Fetal Kidney	kidney
39	chr7:99125800-99126800	ZNF genes & repeats	NHLF	lung
40	chr7:99125800-99127200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:99125800-99127200	Strong transcription	Pancreas	Pancrea
42	chr7:99125800-99128600	Strong transcription	Brain Hippocampus Middle	brain
43	chr7:99125800-99131600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
44	chr7:99125800-99131800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:99125800-99131800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
46	chr7:99125800-99131800	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr7:99125800-99131800	ZNF genes & repeats	Fetal Lung	lung
48	chr7:99125800-99131800	ZNF genes & repeats	Fetal Muscle Leg	muscle
49	chr7:99125800-99132000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:99125800-99132000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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