Variant report

Variant	rs3798929
Chromosome Location	chr6:161609279-161609280
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161601048..161605032-chr6:161608423..161610075,3	K562	blood:
2	chr6:161601048..161604055-chr6:161608351..161610075,3	K562	blood:
3	chr6:161608508..161611578-chr6:161612848..161615127,3	K562	blood:
4	chr6:161607405..161609725-chr6:161623701..161625620,3	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10945719	0.94[ASW][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11756131	0.80[CHB][hapmap];0.87[LWK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs12209184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2314157	0.82[AFR][1000 genomes]
rs3778223	0.97[ASN][1000 genomes]
rs3778224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798927	0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3798928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770491	0.86[LWK][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	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv949397	chr6:161592100-161812932	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2752091	chr6:161592100-161855785	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1029727	chr6:161607680-161814295	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3798929	AGPAT4	cis	cerebellum	SCAN
rs3798929	TAGAP	cis	parietal	SCAN
rs3798929	MAS1	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161585600-161626000	Weak transcription	Right Atrium	heart
2	chr6:161590000-161611600	Weak transcription	HSMMtube	muscle
3	chr6:161591400-161626200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:161591600-161615400	Weak transcription	Fetal Heart	heart
5	chr6:161592000-161609600	Weak transcription	Fetal Brain Male	brain
6	chr6:161599800-161647600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:161600200-161610000	Weak transcription	Primary T cells from cord blood	blood
8	chr6:161600400-161619400	Weak transcription	Fetal Lung	lung
9	chr6:161600400-161626000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:161600600-161613000	Weak transcription	Primary B cells from cord blood	blood
11	chr6:161600600-161613800	Weak transcription	Fetal Brain Female	brain
12	chr6:161601400-161610400	Weak transcription	Aorta	Aorta
13	chr6:161601400-161636200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:161601800-161609400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:161601800-161609800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:161602000-161613800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:161602000-161619400	Weak transcription	Brain Germinal Matrix	brain
18	chr6:161602400-161609800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:161602400-161613800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:161602800-161618600	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:161602800-161626000	Weak transcription	Gastric	stomach
22	chr6:161604000-161609600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:161604000-161610200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:161604400-161609800	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:161605200-161610200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr6:161605200-161612600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:161605400-161610200	Weak transcription	Brain Substantia Nigra	brain
28	chr6:161606200-161615400	Weak transcription	Fetal Kidney	kidney
29	chr6:161607600-161610000	Weak transcription	Brain Anterior Caudate	brain
30	chr6:161607600-161610200	Weak transcription	Esophagus	oesophagus
31	chr6:161607600-161612200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:161607600-161621400	Weak transcription	Adipose Nuclei	Adipose
33	chr6:161607800-161610200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:161607800-161610200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:161607800-161610200	Weak transcription	Lung	lung
36	chr6:161607800-161610200	Weak transcription	Ovary	ovary
37	chr6:161607800-161613800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:161607800-161619200	Weak transcription	NHLF	lung
39	chr6:161607800-161619400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:161607800-161619400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:161607800-161629800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:161607800-161644200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:161608000-161610200	Weak transcription	Brain Angular Gyrus	brain
44	chr6:161608000-161612000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:161608000-161612600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:161608000-161636000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:161608200-161610800	Weak transcription	K562	blood
48	chr6:161608400-161609600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:161608400-161609800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:161608400-161610000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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