Variant report

Variant	rs6824643
Chromosome Location	chr4:175168083-175168084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:175162287..175164616-chr4:175167133..175169493,3	K562	blood:
2	chr4:175166567..175169450-chr4:175175425..175177683,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10034021	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10520275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10565	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11939946	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11944262	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap]
rs11946084	0.88[CEU][hapmap]
rs13101580	0.94[MEX][hapmap]
rs13128257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130276	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13150997	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1508222	0.86[ASN][1000 genomes]
rs17291087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17291128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17291408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17357120	1.00[CHB][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.86[ASN][1000 genomes]
rs1995749	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2332836	0.82[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap]
rs41279509	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287982	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4695915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695922	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6553777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68084371	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6851312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72702217	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7661236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv881449	chr4:174984230-175225452	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6824643	KIAA1712	cis	cerebellum	SCAN
rs6824643	KIAA1712	cis	multi-tissue	Pritchard
rs6824643	CEP44	cis	Thyroid	GTEx
rs6824643	FBXO8	cis	cerebellum	SCAN
rs6824643	FBXO8	cis	parietal	SCAN
rs6824643	KIAA1712	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175147600-175195200	Weak transcription	Psoas Muscle	Psoas
2	chr4:175151400-175192800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:175151800-175169400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:175151800-175181600	Weak transcription	Brain Angular Gyrus	brain
5	chr4:175152600-175169400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:175152600-175176400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:175153000-175174200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:175153200-175169000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr4:175153200-175174600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:175153200-175184000	Weak transcription	Lung	lung
11	chr4:175153400-175191600	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:175154200-175204000	Weak transcription	Aorta	Aorta
13	chr4:175154200-175204200	Weak transcription	Esophagus	oesophagus
14	chr4:175154400-175186200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:175154400-175202400	Weak transcription	Gastric	stomach
16	chr4:175155400-175185000	Weak transcription	Spleen	Spleen
17	chr4:175155600-175177000	Weak transcription	Fetal Kidney	kidney
18	chr4:175155600-175178200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:175155800-175186600	Weak transcription	Fetal Brain Female	brain
20	chr4:175156200-175169600	Weak transcription	HSMMtube	muscle
21	chr4:175156200-175174400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr4:175156200-175174400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:175156600-175181600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:175156800-175177000	Weak transcription	Brain Substantia Nigra	brain
25	chr4:175156800-175183400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:175157000-175179600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr4:175157000-175181400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr4:175157000-175184000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:175158800-175176200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:175158800-175178600	Weak transcription	Left Ventricle	heart
31	chr4:175158800-175202000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:175159000-175177000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:175159000-175177000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr4:175159000-175178600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:175159000-175178600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr4:175159000-175180400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:175159000-175184000	Weak transcription	Ovary	ovary
38	chr4:175159000-175184200	Weak transcription	Fetal Lung	lung
39	chr4:175159600-175178400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:175159800-175199800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:175160200-175177000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:175160400-175176800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr4:175160400-175178600	Weak transcription	Fetal Intestine Large	intestine
44	chr4:175160800-175176800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:175161000-175178600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:175161000-175192400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr4:175161200-175177200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:175161200-175178600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr4:175161600-175177800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr4:175161600-175178400	Weak transcription	Liver	Liver

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