Variant report

Variant	rs12527778
Chromosome Location	chr6:86254522-86254523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86253602..86255869-chr6:86388137..86389916,2	K562	blood:
2	chr6:86254209..86255785-chr6:86263781..86265838,2	K562	blood:
3	chr6:86252970..86257934-chr6:86299533..86304034,5	K562	blood:

Variant related genes	Relation type
ENSG00000135317	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11961028	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12524944	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16876341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4626396	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707208	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised 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	15 gene(s)	inside rSNPs	diseases
6	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv463937	chr6:86114766-86264374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv604092	chr6:86114766-86264374	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv886333	chr6:86199243-86289415	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv463939	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv470839	chr6:86205323-86279737	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv604093	chr6:86205323-86279737	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
14	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
15	nsv516516	chr6:86234835-86278691	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12527778	IBTK	cis	cerebellum	SCAN
rs12527778	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs12527778	PRSS35	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86208800-86284600	Weak transcription	Small Intestine	intestine
2	chr6:86208800-86289200	Weak transcription	Pancreas	Pancrea
3	chr6:86218000-86260200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:86218400-86266200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:86220200-86257200	Weak transcription	Fetal Heart	heart
6	chr6:86221800-86285800	Weak transcription	Fetal Brain Male	brain
7	chr6:86222600-86289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:86223200-86260200	Weak transcription	Lung	lung
9	chr6:86223400-86262800	Weak transcription	Stomach Mucosa	stomach
10	chr6:86223400-86285000	Weak transcription	Brain Substantia Nigra	brain
11	chr6:86223800-86262600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:86224000-86255800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:86224000-86279000	Weak transcription	NHLF	lung
14	chr6:86224200-86302600	Weak transcription	Colonic Mucosa	Colon
15	chr6:86230000-86263000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:86231200-86285000	Weak transcription	Hela-S3	cervix
17	chr6:86233000-86257000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:86233400-86257800	Weak transcription	Ovary	ovary
19	chr6:86233400-86262200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:86233600-86262400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:86233800-86289200	Weak transcription	Spleen	Spleen
22	chr6:86234000-86261000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:86236600-86255600	Weak transcription	HSMMtube	muscle
24	chr6:86236600-86279000	Weak transcription	HMEC	breast
25	chr6:86241400-86283600	Weak transcription	Fetal Kidney	kidney
26	chr6:86243200-86285200	Weak transcription	Psoas Muscle	Psoas
27	chr6:86243200-86286000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:86243400-86256800	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:86243400-86257000	Weak transcription	A549	lung
30	chr6:86243400-86269600	Weak transcription	Brain Anterior Caudate	brain
31	chr6:86243400-86301400	Weak transcription	Thymus	Thymus
32	chr6:86243600-86256400	Weak transcription	K562	blood
33	chr6:86243600-86256800	Weak transcription	GM12878-XiMat	blood
34	chr6:86243600-86285000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:86243600-86285800	Weak transcription	Fetal Brain Female	brain
36	chr6:86243600-86286200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:86243800-86284800	Weak transcription	Brain Angular Gyrus	brain
38	chr6:86244000-86262800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:86244000-86265400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:86244200-86279000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:86244200-86286000	Weak transcription	Right Ventricle	heart
42	chr6:86244200-86289200	Weak transcription	Gastric	stomach
43	chr6:86244400-86281000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:86245000-86255400	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:86245800-86255600	Weak transcription	Fetal Thymus	thymus
46	chr6:86245800-86261000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:86246400-86279000	Weak transcription	NHEK	skin
48	chr6:86246600-86265000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr6:86246600-86270800	Weak transcription	HUVEC	blood vessel
50	chr6:86246600-86274200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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