Variant report

Variant	rs6838291
Chromosome Location	chr4:7917806-7917807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10029941	0.82[CHB][hapmap]
rs13109291	0.82[CHB][hapmap]
rs1344223	0.82[CHB][hapmap]
rs1557817	1.00[CHB][hapmap]
rs17770936	0.90[CEU][hapmap]
rs2018399	1.00[CHB][hapmap]
rs2107182	0.82[CHB][hapmap]
rs2385914	0.82[CHB][hapmap]
rs28393652	0.88[ASN][1000 genomes]
rs28418478	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28451112	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28468456	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28508479	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28612887	0.88[ASN][1000 genomes]
rs28621561	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28638094	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28657375	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28657625	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28662492	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28728216	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28861809	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4075363	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4234829	0.82[CHB][hapmap]
rs4377592	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4383619	0.91[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4388087	0.91[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4404542	0.91[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4413405	0.91[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4473655	0.83[CEU][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap]
rs4496581	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4496582	0.88[ASN][1000 genomes]
rs4552460	0.91[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs4605652	0.80[AMR][1000 genomes]
rs4623000	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6446619	0.82[CHB][hapmap]
rs6827395	1.00[CHB][hapmap]
rs6828807	0.82[CHB][hapmap]
rs6829473	0.82[CHB][hapmap]
rs6852990	0.82[CHB][hapmap]
rs756255	0.82[CHB][hapmap]
rs7698368	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6838291	PPP2R2C	cis	cerebellum	SCAN
rs6838291	AFAP1	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
3	chr4:7909200-7925400	Weak transcription	Hela-S3	cervix
4	chr4:7912000-7918000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:7912000-7931200	Weak transcription	Aorta	Aorta
6	chr4:7912800-7931200	Weak transcription	Gastric	stomach
7	chr4:7913000-7927600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:7913000-7930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:7913000-7931000	Weak transcription	Fetal Intestine Large	intestine
10	chr4:7913200-7918200	Weak transcription	Colonic Mucosa	Colon
11	chr4:7913200-7919400	Weak transcription	Right Atrium	heart
12	chr4:7913200-7919600	Weak transcription	Lung	lung
13	chr4:7913200-7926400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:7913400-7918200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:7913400-7918800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:7913400-7919800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:7913600-7918000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr4:7913600-7926200	Weak transcription	Fetal Brain Female	brain
19	chr4:7913600-7927200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:7913600-7930400	Weak transcription	NHEK	skin
21	chr4:7913800-7919600	Weak transcription	Adipose Nuclei	Adipose
22	chr4:7913800-7925600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:7914000-7918400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:7914000-7919200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:7914000-7919400	Weak transcription	Fetal Intestine Small	intestine
26	chr4:7914000-7926800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:7914200-7918200	Weak transcription	Brain Germinal Matrix	brain
28	chr4:7914200-7918800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:7914200-7919600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:7914200-7919600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:7914200-7925800	Weak transcription	HSMMtube	muscle
32	chr4:7914200-7930800	Weak transcription	Fetal Kidney	kidney
33	chr4:7914400-7918000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:7914400-7918000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr4:7914400-7925600	Weak transcription	HSMM	muscle
36	chr4:7914800-7918600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:7914800-7919200	Weak transcription	NHLF	lung
38	chr4:7914800-7919600	Weak transcription	HMEC	breast
39	chr4:7915000-7918200	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:7915000-7918200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:7915000-7918200	Weak transcription	Fetal Stomach	stomach
42	chr4:7915000-7918200	Weak transcription	HUVEC	blood vessel
43	chr4:7915000-7926000	Weak transcription	Fetal Muscle Leg	muscle
44	chr4:7915000-7928200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:7915000-7930400	Weak transcription	Fetal Lung	lung
46	chr4:7915200-7918400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:7916200-7919600	Enhancers	Fetal Heart	heart
48	chr4:7916200-7921200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:7916400-7918000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:7916400-7918000	Weak transcription	A549	lung

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