Variant report

Variant	rs3798940
Chromosome Location	chr6:161657187-161657188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr6:161656923-161657625	GM12878	blood:	n/a	n/a
2	NFIC	chr6:161656796-161657740	GM12878	blood:	n/a	n/a
3	BATF	chr6:161657159-161657592	GM12878	blood:	n/a	n/a
4	EP300	chr6:161657158-161657417	GM12878	blood:	n/a	n/a
5	RELA	chr6:161656960-161657701	GM12891	blood:	n/a	n/a
6	MTA3	chr6:161657065-161657701	GM12878	blood:	n/a	n/a
7	STAT5A	chr6:161657161-161657544	GM12878	blood:	n/a	n/a
8	STAT5A	chr6:161657139-161657616	GM12878	blood:	n/a	chr6:161657533-161657556
9	RUNX3	chr6:161657164-161657579	GM12878	blood:	n/a	n/a
10	NFATC1	chr6:161657137-161657658	GM12878	blood:	n/a	n/a
11	ATF2	chr6:161656868-161657635	GM12878	blood:	n/a	n/a
12	MEF2C	chr6:161656919-161657624	GM12878	blood:	n/a	n/a
13	NFIC	chr6:161656956-161657627	GM12878	blood:	n/a	n/a
14	BHLHE40	chr6:161657185-161657583	GM12878	blood:	n/a	n/a
15	FOXM1	chr6:161657082-161657648	GM12878	blood:	n/a	n/a
16	IRF4	chr6:161657123-161657663	GM12878	blood:	n/a	n/a
17	RELA	chr6:161656991-161657619	GM18505	blood:	n/a	n/a
18	MTA3	chr6:161657156-161657604	GM12878	blood:	n/a	n/a
19	RELA	chr6:161657030-161657603	GM12878	blood:	n/a	n/a
20	ATF2	chr6:161657090-161657632	GM12878	blood:	n/a	n/a
21	RUNX3	chr6:161657153-161657685	GM12878	blood:	n/a	n/a
22	CEBPB	chr6:161657043-161657687	GM12878	blood:	n/a	n/a
23	MEF2A	chr6:161656945-161657617	GM12878	blood:	n/a	n/a
24	ZNF384	chr6:161657152-161657488	GM12878	blood:	n/a	n/a
25	CREB1	chr6:161656927-161657655	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:161585978..161588627-chr6:161656198..161658945,2	K562	blood:
2	chr6:161494196..161496885-chr6:161657135..161659498,2	K562	blood:
3	chr6:161633305..161636291-chr6:161657076..161658603,2	K562	blood:
4	chr6:161656907..161658556-chr6:161664328..161666054,2	K562	blood:

No data

Variant related genes	Relation type
AGPAT4	TF binding region
ENSG00000085511	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs3778229	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6455710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455711	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6455712	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6941651	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7738367	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7763278	0.85[CEU][hapmap];0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
6	nsv1030623	chr6:161611170-161796985	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv538494	chr6:161611170-161796985	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv886818	chr6:161629323-161723705	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv481931	chr6:161647026-161961906	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv533149	chr6:161653240-161769727	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3798940	C16orf81	trans	cerebellum	SCAN
rs3798940	AGPAT4	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161638200-161693800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:161638600-161668000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:161639000-161666200	Weak transcription	Aorta	Aorta
4	chr6:161639200-161664400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:161647200-161663200	Weak transcription	Thymus	Thymus
6	chr6:161648000-161660600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:161649400-161657400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:161649400-161662800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:161649600-161693800	Weak transcription	Right Atrium	heart
10	chr6:161650000-161662800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr6:161650400-161658000	Enhancers	Brain Substantia Nigra	brain
12	chr6:161651000-161658800	Weak transcription	Esophagus	oesophagus
13	chr6:161651000-161663400	Weak transcription	Lung	lung
14	chr6:161651000-161677000	Weak transcription	Spleen	Spleen
15	chr6:161651200-161666000	Weak transcription	Primary T cells from cord blood	blood
16	chr6:161653200-161664200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:161653400-161659400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:161653600-161657600	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr6:161653600-161658200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:161653600-161660800	Weak transcription	Fetal Kidney	kidney
21	chr6:161653800-161657400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr6:161653800-161658200	Enhancers	Brain Germinal Matrix	brain
23	chr6:161653800-161659600	Enhancers	Fetal Heart	heart
24	chr6:161653800-161693800	Weak transcription	Primary B cells from cord blood	blood
25	chr6:161654000-161664000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:161654200-161657400	Enhancers	Fetal Brain Female	brain
27	chr6:161654600-161657600	Enhancers	Fetal Stomach	stomach
28	chr6:161654600-161657600	Enhancers	K562	blood
29	chr6:161654800-161657600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:161654800-161657600	Enhancers	Brain Cingulate Gyrus	brain
31	chr6:161655000-161657400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr6:161655000-161657600	Enhancers	Fetal Brain Male	brain
33	chr6:161655000-161657800	Enhancers	Rectal Smooth Muscle	rectum
34	chr6:161655200-161657600	Enhancers	Brain Anterior Caudate	brain
35	chr6:161655200-161659600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr6:161655600-161657400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr6:161655800-161657200	Weak transcription	HSMMtube	muscle
38	chr6:161655800-161658200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:161655800-161658800	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:161655800-161659400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:161655800-161663800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr6:161655800-161680400	Weak transcription	HMEC	breast
43	chr6:161656000-161657600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:161656000-161657600	Enhancers	Brain Hippocampus Middle	brain
45	chr6:161656000-161658200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:161656000-161658200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:161656000-161659600	Weak transcription	NHEK	skin
48	chr6:161656000-161661200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:161656000-161663600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:161656000-161664200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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