Variant report

Variant	rs4348312
Chromosome Location	chr6:36832028-36832029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36830142..36832721-chr6:36892785..36895215,2	K562	blood:
2	chr6:36817709..36820546-chr6:36830678..36833403,3	MCF-7	breast:
3	chr6:36584813..36586612-chr6:36830505..36832911,2	K562	blood:
4	chr6:36831717..36834035-chr6:36985083..36987828,2	K562	blood:
5	chr6:36749029..36752383-chr6:36830307..36832298,3	MCF-7	breast:
6	chr6:36828665..36833827-chr6:36838293..36844932,14	MCF-7	breast:
7	chr6:36561665..36563216-chr6:36830142..36832208,2	MCF-7	breast:
8	chr6:36813865..36816350-chr6:36831704..36833513,2	MCF-7	breast:
9	chr6:36719279..36721596-chr6:36829791..36832062,2	MCF-7	breast:
10	chr6:36799434..36803274-chr6:36828928..36832166,3	MCF-7	breast:
11	chr6:36752311..36754452-chr6:36830186..36832199,2	K562	blood:
12	chr6:36830465..36834114-chr6:36840024..36843322,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198663	Chromatin interaction
ENSG00000137168	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10456445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456447	0.89[AMR][1000 genomes]
rs10456448	0.82[ASN][1000 genomes]
rs10947646	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11964396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111291	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191780	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12193721	0.82[ASN][1000 genomes]
rs12195012	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12215873	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12524018	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12524422	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12524649	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525180	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525540	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12526699	0.97[EUR][1000 genomes]
rs12527905	0.81[AMR][1000 genomes]
rs12529199	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs12529769	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17374068	1.00[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.85[EUR][1000 genomes]
rs17552561	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864753	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs236382	0.85[CEU][hapmap]
rs35694858	0.80[EUR][1000 genomes]
rs41272192	0.90[ASN][1000 genomes]
rs41408445	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714013	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4714022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55681762	0.90[EUR][1000 genomes]
rs55913388	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55928881	0.82[ASN][1000 genomes]
rs56240344	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56302344	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66474948	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66566790	0.90[EUR][1000 genomes]
rs67273613	0.97[EUR][1000 genomes]
rs68042914	0.91[EUR][1000 genomes]
rs72846046	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72846078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73416282	0.85[EUR][1000 genomes]
rs7745555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762601	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4348312	PNPLA1	cis	parietal	SCAN
rs4348312	C6orf89	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36817000-36841400	Weak transcription	Colonic Mucosa	Colon
2	chr6:36817200-36833400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:36817200-36841200	Weak transcription	Fetal Brain Male	brain
4	chr6:36817200-36842000	Weak transcription	Stomach Mucosa	stomach
5	chr6:36819000-36840400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:36819400-36834000	Strong transcription	Dnd41	blood
7	chr6:36819400-36841800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:36819600-36833400	Strong transcription	Primary T cells from cord blood	blood
9	chr6:36819800-36839800	Strong transcription	Fetal Thymus	thymus
10	chr6:36821000-36841400	Weak transcription	Small Intestine	intestine
11	chr6:36821800-36839800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:36821800-36841400	Weak transcription	HSMMtube	muscle
13	chr6:36823600-36841400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:36823800-36833600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:36824200-36833800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:36824400-36832400	Weak transcription	HSMM	muscle
17	chr6:36824400-36836600	Weak transcription	Adipose Nuclei	Adipose
18	chr6:36824600-36834000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:36824600-36838600	Weak transcription	Psoas Muscle	Psoas
20	chr6:36825000-36834000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:36826200-36839800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:36826400-36833200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:36826400-36841200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:36826800-36840000	Strong transcription	Fetal Stomach	stomach
25	chr6:36826800-36841400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:36827000-36834600	Weak transcription	Ovary	ovary
27	chr6:36827000-36841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:36827000-36841400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr6:36827000-36841400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:36827400-36834600	Strong transcription	Fetal Muscle Leg	muscle
31	chr6:36827600-36839400	Strong transcription	HepG2	liver
32	chr6:36827600-36840400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:36827800-36840600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:36828000-36832800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:36828000-36833000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr6:36828000-36838200	Strong transcription	Hela-S3	cervix
37	chr6:36828000-36838800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr6:36828000-36841400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:36828200-36839800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr6:36828200-36841600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:36828600-36833200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr6:36828600-36836600	Strong transcription	Primary B cells from cord blood	blood
43	chr6:36828600-36841000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:36828800-36841200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:36829000-36836000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:36829000-36840400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:36829200-36837200	Strong transcription	Fetal Intestine Small	intestine
48	chr6:36829400-36833400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:36829800-36832400	Strong transcription	Lung	lung
50	chr6:36829800-36833000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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