Variant report

Variant	rs3176334
Chromosome Location	chr6:36648364-36648365
allele	C/T
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:25)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:36592351..36593048-chr6:36648313..36648819,2	K562	blood:
2	chr6:36578466..36580870-chr6:36647924..36649824,2	MCF-7	breast:
3	chr6:36584612..36585297-chr6:36648004..36648751,2	MCF-7	breast:
4	chr6:36561535..36562422-chr6:36647947..36648663,2	K562	blood:
5	chr6:36646638..36649501-chr6:36950264..36953112,2	MCF-7	breast:
6	chr6:36589971..36596625-chr6:36645571..36650576,10	K562	blood:
7	chr6:36644838..36653438-chr6:36718524..36730954,23	MCF-7	breast:
8	chr6:36564965..36566976-chr6:36648126..36649999,2	K562	blood:
9	chr6:27100904..27101438-chr6:36648004..36648546,2	Hela-S3	cervix:
10	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
11	chr6:36560711..36564837-chr6:36645733..36649715,9	K562	blood:
12	chr6:36560285..36563984-chr6:36645642..36649715,8	K562	blood:
13	chr6:36559895..36571260-chr6:36642384..36648914,19	MCF-7	breast:
14	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
15	chr6:36590986..36591856-chr6:36647878..36648875,10	K562	blood:
16	chr6:36590922..36591850-chr6:36647865..36648817,7	MCF-7	breast:
17	chr6:36646719..36650011-chr6:36657952..36660291,4	MCF-7	breast:
18	chr6:36570219..36573404-chr6:36646918..36650255,3	K562	blood:
19	chr6:36647044..36648855-chr6:36663270..36664993,2	MCF-7	breast:
20	chr6:36571904..36574235-chr6:36647480..36649037,2	K562	blood:
21	chr6:36518339..36520561-chr6:36646946..36648999,2	K562	blood:
22	chr6:36590906..36591946-chr6:36647029..36648637,8	MCF-7	breast:
23	chr6:36589213..36595227-chr6:36645571..36651666,9	K562	blood:
24	chr6:36560169..36564521-chr6:36645252..36648947,8	MCF-7	breast:
25	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB44-3	chr6:36648251-36648457	NONHSAT112229

No data

Variant related genes	Relation type
ENSG00000124772	Chromatin interaction
ENSG00000263894	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10807170	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs2395655	0.92[CEU][hapmap]
rs3176320	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]
rs3176323	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4135240	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711457	0.86[JPT][hapmap]
rs4713996	0.85[JPT][hapmap]
rs4713999	0.87[TSI][hapmap]
rs4714001	0.85[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs733590	0.84[CEU][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9394368	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
rs3176334	PI16	cis	parietal	SCAN
rs3176334	SNRPC	cis	cerebellum	SCAN
rs3176334	LHFPL5	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36645600-36648600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:36646000-36648400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:36646000-36648400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:36646000-36648600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
5	chr6:36646000-36648600	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr6:36646000-36648800	Active TSS	Aorta	Aorta
7	chr6:36646000-36648800	Active TSS	Psoas Muscle	Psoas
8	chr6:36646000-36649000	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr6:36646000-36650200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr6:36646200-36648400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:36646200-36648400	Active TSS	Muscle Satellite Cultured Cells	--
12	chr6:36646200-36648400	Active TSS	Liver	Liver
13	chr6:36646200-36648400	Active TSS	Brain Angular Gyrus	brain
14	chr6:36646200-36648400	Active TSS	Hela-S3	cervix
15	chr6:36646200-36648400	Active TSS	NHDF-Ad	bronchial
16	chr6:36646200-36648400	Active TSS	Osteobl	bone
17	chr6:36646200-36648600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:36646200-36648600	Active TSS	Brain Anterior Caudate	brain
19	chr6:36646200-36648600	Active TSS	Colon Smooth Muscle	Colon
20	chr6:36646200-36648600	Active TSS	Duodenum Mucosa	Duodenum
21	chr6:36646200-36648600	Active TSS	Fetal Kidney	kidney
22	chr6:36646200-36648600	Active TSS	A549	lung
23	chr6:36646200-36648600	Active TSS	HUVEC	blood vessel
24	chr6:36646200-36648800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:36646200-36648800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr6:36646200-36648800	Active TSS	Right Ventricle	heart
27	chr6:36646200-36649000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr6:36646200-36649000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr6:36646200-36649000	Active TSS	Esophagus	oesophagus
30	chr6:36646200-36649000	Active TSS	Ovary	ovary
31	chr6:36646200-36649000	Flanking Bivalent TSS/Enh	Dnd41	blood
32	chr6:36646200-36649600	Active TSS	HSMM	muscle
33	chr6:36646200-36649800	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr6:36646200-36650200	Active TSS	HSMMtube	muscle
35	chr6:36646400-36648400	Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr6:36646400-36648400	Active TSS	Small Intestine	intestine
37	chr6:36646400-36648400	Active TSS	Stomach Mucosa	stomach
38	chr6:36646400-36648400	Active TSS	HMEC	breast
39	chr6:36646400-36648400	Active TSS	NH-A	brain
40	chr6:36646400-36648400	Active TSS	NHEK	skin
41	chr6:36646400-36648600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:36646400-36648600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:36646400-36648600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:36646400-36648600	Active TSS	Left Ventricle	heart
45	chr6:36646400-36648600	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr6:36646400-36648600	Active TSS	GM12878-XiMat	blood
47	chr6:36646400-36648800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
48	chr6:36646400-36648800	Active TSS	NHLF	lung
49	chr6:36646400-36649000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:36646400-36649000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

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