Variant report

Variant	rs6829993
Chromosome Location	chr4:76631063-76631064
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76603137..76606116-chr4:76628851..76631613,2	K562	blood:
2	chr4:76578842..76581813-chr4:76628812..76631352,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10016782	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10028291	0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10031616	0.86[EUR][1000 genomes]
rs10033315	0.80[EUR][1000 genomes]
rs10212995	0.81[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs11097075	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11097112	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs11097113	0.80[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs11728073	0.80[EUR][1000 genomes]
rs11730896	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11932454	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11938067	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs11943497	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12505149	0.82[EUR][1000 genomes]
rs13102733	0.84[EUR][1000 genomes]
rs13110602	0.81[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs13133144	0.80[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs13133472	0.80[EUR][1000 genomes]
rs13145290	0.80[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs13147276	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2055997	0.94[JPT][hapmap]
rs2271472	0.80[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs2869175	0.85[EUR][1000 genomes]
rs3796481	0.80[EUR][1000 genomes]
rs4859404	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4859405	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859406	0.81[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4859408	0.87[CHD][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4859409	0.80[EUR][1000 genomes]
rs4859549	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859552	0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs4859554	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs4859555	0.82[EUR][1000 genomes]
rs6531901	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs6843016	0.81[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs6844014	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6845147	0.80[EUR][1000 genomes]
rs6847333	0.81[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs7655464	0.80[CEU][hapmap];0.84[CHD][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7661037	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7665517	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs905954	0.80[EUR][1000 genomes]
rs987561	0.81[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6829993	FAM47E	cis	parietal	SCAN
rs6829993	CXCL10	cis	parietal	SCAN
rs6829993	PPEF2	cis	parietal	SCAN
rs6829993	CCNG2	cis	cerebellum	SCAN
rs6829993	PAQR3	cis	cerebellum	SCAN
rs6829993	SCARB2	cis	parietal	SCAN
rs6829993	CDKL2	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76599200-76640000	Weak transcription	Aorta	Aorta
2	chr4:76599600-76639800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:76599600-76639800	Weak transcription	Brain Angular Gyrus	brain
4	chr4:76599600-76639800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:76599600-76647600	Weak transcription	Fetal Brain Female	brain
6	chr4:76600400-76640000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:76605800-76633200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:76607400-76640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:76613800-76639000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:76613800-76639600	Weak transcription	Ovary	ovary
11	chr4:76615600-76639800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:76615600-76639800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:76615800-76639000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:76616000-76640000	Weak transcription	Lung	lung
15	chr4:76618200-76635000	Weak transcription	Adipose Nuclei	Adipose
16	chr4:76618400-76639000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:76619400-76633400	Weak transcription	Fetal Kidney	kidney
18	chr4:76620000-76640000	Weak transcription	Brain Germinal Matrix	brain
19	chr4:76620400-76639600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:76620600-76631400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:76620600-76640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:76621000-76640600	Weak transcription	Right Ventricle	heart
23	chr4:76621800-76642400	Weak transcription	Left Ventricle	heart
24	chr4:76622000-76639400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:76622200-76639800	Weak transcription	HSMMtube	muscle
26	chr4:76623800-76647600	Weak transcription	Fetal Heart	heart
27	chr4:76624200-76640600	Weak transcription	Fetal Thymus	thymus
28	chr4:76624400-76633400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr4:76624400-76647200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr4:76624400-76647800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:76624600-76634600	Weak transcription	Primary B cells from cord blood	blood
32	chr4:76624600-76646800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr4:76624800-76633200	Weak transcription	Primary T cells from cord blood	blood
34	chr4:76624800-76634600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr4:76624800-76634600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:76624800-76634600	Weak transcription	GM12878-XiMat	blood
37	chr4:76624800-76634800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr4:76624800-76647600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr4:76626400-76631600	Enhancers	Fetal Intestine Large	intestine
40	chr4:76627800-76631600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr4:76628000-76639800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:76628400-76639600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:76628600-76633200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr4:76628600-76633400	Weak transcription	Psoas Muscle	Psoas
45	chr4:76628600-76633400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr4:76628600-76640000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr4:76628800-76635600	Weak transcription	A549	lung
48	chr4:76628800-76642200	Weak transcription	Fetal Stomach	stomach
49	chr4:76629000-76633200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr4:76629000-76633200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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