Variant report

Variant	rs3176320
Chromosome Location	chr6:36646788-36646789
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:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36645391..36647920-chr6:36680659..36684331,3	MCF-7	breast:
2	chr22:29137882..29138609-chr6:36646475..36646984,2	Hela-S3	cervix:
3	chr6:36646638..36649501-chr6:36950264..36953112,2	MCF-7	breast:
4	chr6:36646406..36647008-chr9:130213190..130213761,2	Hela-S3	cervix:
5	chr6:36589971..36596625-chr6:36645571..36650576,10	K562	blood:
6	chr17:57914670..57916833-chr6:36645394..36647964,3	MCF-7	breast:
7	chr6:36644838..36653438-chr6:36718524..36730954,23	MCF-7	breast:
8	chr1:40042208..40042835-chr6:36646343..36646854,2	HCT-116	colon:
9	chr6:36644040..36648031-chr6:36680924..36685784,5	MCF-7	breast:
10	chr6:36646643..36648189-chr6:36817431..36818959,2	MCF-7	breast:
11	chr17:56707748..56709290-chr6:36645821..36647810,2	MCF-7	breast:
12	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
13	chr6:36560711..36564837-chr6:36645733..36649715,9	K562	blood:
14	chr6:36560285..36563984-chr6:36645642..36649715,8	K562	blood:
15	chr6:36559895..36571260-chr6:36642384..36648914,19	MCF-7	breast:
16	chr6:36606453..36608701-chr6:36645452..36648033,2	MCF-7	breast:
17	chr6:36646585..36648136-chr6:36723645..36726426,2	K562	blood:
18	chr10:11865096..11865789-chr6:36646486..36647024,2	Hela-S3	cervix:
19	chr6:36640651..36642338-chr6:36646391..36648359,2	K562	blood:
20	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
21	chr6:36646719..36650011-chr6:36657952..36660291,4	MCF-7	breast:
22	chr6:36589213..36595227-chr6:36645571..36651666,9	K562	blood:
23	chr6:36560169..36564521-chr6:36645252..36648947,8	MCF-7	breast:
24	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213500	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000090621	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000197958	Chromatin interaction
ENSG00000255587	Chromatin interaction
ENSG00000148426	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000112081	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000238554	Chromatin interaction
ENSG00000263894	Chromatin interaction
ENSG00000124772	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10807170	0.86[JPT][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap]
rs2395655	0.96[CEU][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3176323	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3176334	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4135240	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711457	0.86[JPT][hapmap];0.80[MEX][hapmap]
rs4713996	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs4713999	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs4714001	0.85[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6930083	0.81[CEU][hapmap]
rs733590	0.88[CEU][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9394368	0.80[CEU][hapmap];0.85[JPT][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	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv885807	chr6:36645696-36651889	Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
4	nsv602948	chr6:36646788-36651889	Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers	Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
5	nsv602949	chr6:36646788-36652067	Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3176320	SNRPC	cis	cerebellum	SCAN
rs3176320	LHFPL5	cis	cerebellum	SCAN
rs3176320	PI16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36644200-36647600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:36645600-36647000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
3	chr6:36645600-36648600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr6:36645800-36646800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:36645800-36647400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr6:36646000-36646800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:36646000-36646800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:36646000-36646800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:36646000-36647000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:36646000-36647200	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr6:36646000-36647400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr6:36646000-36647400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr6:36646000-36647400	Flanking Active TSS	Colonic Mucosa	Colon
14	chr6:36646000-36647400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
15	chr6:36646000-36647600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr6:36646000-36647800	Bivalent Enhancer	Fetal Brain Male	brain
17	chr6:36646000-36648000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr6:36646000-36648000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr6:36646000-36648000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr6:36646000-36648400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:36646000-36648400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:36646000-36648600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
23	chr6:36646000-36648600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr6:36646000-36648800	Active TSS	Aorta	Aorta
25	chr6:36646000-36648800	Active TSS	Psoas Muscle	Psoas
26	chr6:36646000-36649000	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr6:36646000-36650200	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr6:36646200-36646800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:36646200-36647000	Active TSS	Brain Cingulate Gyrus	brain
30	chr6:36646200-36647000	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr6:36646200-36647000	Active TSS	Rectal Smooth Muscle	rectum
32	chr6:36646200-36647000	Active TSS	Monocytes-CD14+_RO01746	blood
33	chr6:36646200-36647200	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr6:36646200-36647400	Flanking Active TSS	K562	blood
35	chr6:36646200-36647600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr6:36646200-36647600	Flanking Bivalent TSS/Enh	Thymus	Thymus
37	chr6:36646200-36648000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
38	chr6:36646200-36648200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:36646200-36648400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:36646200-36648400	Active TSS	Muscle Satellite Cultured Cells	--
41	chr6:36646200-36648400	Active TSS	Liver	Liver
42	chr6:36646200-36648400	Active TSS	Brain Angular Gyrus	brain
43	chr6:36646200-36648400	Active TSS	Hela-S3	cervix
44	chr6:36646200-36648400	Active TSS	NHDF-Ad	bronchial
45	chr6:36646200-36648400	Active TSS	Osteobl	bone
46	chr6:36646200-36648600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:36646200-36648600	Active TSS	Brain Anterior Caudate	brain
48	chr6:36646200-36648600	Active TSS	Colon Smooth Muscle	Colon
49	chr6:36646200-36648600	Active TSS	Duodenum Mucosa	Duodenum
50	chr6:36646200-36648600	Active TSS	Fetal Kidney	kidney

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