Variant report

Variant	rs11155639
Chromosome Location	chr6:149637690-149637691
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr6:149637125-149639723	IMR90	lung:	n/a	chr6:149639590-149639599 chr6:149639537-149639547
2	POLR2A	chr6:149636134-149639393	K562	blood:	n/a	n/a
3	MXI1	chr6:149637512-149637706	K562	blood:	n/a	n/a
4	POLR2A	chr6:149637413-149638870	GM12891	blood:	n/a	n/a
5	SPI1	chr6:149637223-149637777	HL-60	blood:	n/a	chr6:149637468-149637481 chr6:149637469-149637482 chr6:149637468-149637481
6	MTA3	chr6:149637597-149638802	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:149637615-149639597	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149349779..149353985-chr6:149637379..149639962,5	MCF-7	breast:
2	chr6:149635359..149638022-chr6:149700186..149702826,2	K562	blood:
3	chr6:149637077..149638837-chr6:149727129..149729209,2	K562	blood:
4	chr6:149557890..149560221-chr6:149637001..149638608,2	MCF-7	breast:
5	chr6:149409902..149411675-chr6:149636224..149638635,2	K562	blood:
6	chr6:149406954..149409794-chr6:149636560..149638477,3	MCF-7	breast:
7	chr6:149636797..149639661-chr6:149663144..149666590,3	K562	blood:
8	chr6:149397256..149399835-chr6:149636593..149638648,2	MCF-7	breast:
9	chr6:149516981..149518503-chr6:149637137..149638798,2	MCF-7	breast:
10	chr6:149625453..149629470-chr6:149636058..149640474,5	MCF-7	breast:
11	chr6:149636340..149638301-chr6:150416961..150418644,2	K562	blood:

No data

Variant related genes	Relation type
TAB2	TF binding region
ENSG00000055208	Chromatin interaction
ENSG00000216265	Chromatin interaction
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11155641	0.87[CHB][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11155644	0.81[EUR][1000 genomes]
rs11964335	0.81[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs13219868	0.82[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs1446556	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1900300	0.82[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs237012	0.82[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap]
rs237016	0.82[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs237019	0.91[CHB][hapmap]
rs237024	0.92[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs237025	0.82[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs237026	0.81[CEU][hapmap];0.93[CHB][hapmap];0.80[EUR][1000 genomes]
rs237028	0.81[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap]
rs237029	0.80[EUR][1000 genomes]
rs237035	0.82[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs372205	0.80[TSI][hapmap]
rs4895787	0.81[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs6570963	0.81[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs6570964	0.82[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs6922130	0.93[CHB][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap]
rs6942381	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs7752555	0.81[EUR][1000 genomes]
rs7753269	0.81[EUR][1000 genomes]
rs805026	0.82[CEU][hapmap];0.93[CHB][hapmap];0.81[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	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1015360	chr6:149609804-149649982	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3377797	chr6:149637284-149640632	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
5	esv3365966	chr6:149637634-149640707	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11155639	SHPRH	cis	cerebellum	SCAN
rs11155639	LRP11	cis	cerebellum	SCAN
rs11155639	SUMO4	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149628000-149637800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:149636600-149637800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:149636600-149637800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:149637000-149637800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:149637200-149637800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:149637200-149637800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:149637200-149637800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:149637200-149637800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr6:149637200-149639800	Active TSS	K562	blood
10	chr6:149637200-149640000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:149637200-149640200	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr6:149637200-149640200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:149637200-149640400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr6:149637200-149640400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:149637200-149640800	Active TSS	A549	lung
16	chr6:149637200-149641000	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr6:149637400-149637800	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr6:149637400-149637800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr6:149637400-149637800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr6:149637400-149637800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr6:149637400-149637800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr6:149637400-149637800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:149637400-149637800	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr6:149637400-149637800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr6:149637400-149637800	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr6:149637400-149637800	Enhancers	Stomach Mucosa	stomach
27	chr6:149637400-149637800	Flanking Active TSS	HepG2	liver
28	chr6:149637400-149637800	Flanking Active TSS	HMEC	breast
29	chr6:149637400-149637800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr6:149637400-149637800	Flanking Active TSS	NHEK	skin
31	chr6:149637400-149638000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr6:149637400-149638000	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr6:149637400-149638000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr6:149637400-149638000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr6:149637400-149638000	Flanking Active TSS	Dnd41	blood
36	chr6:149637400-149638200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:149637400-149638400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:149637400-149639600	Active TSS	Fetal Muscle Leg	muscle
39	chr6:149637400-149639600	Active TSS	Psoas Muscle	Psoas
40	chr6:149637400-149639800	Active TSS	Thymus	Thymus
41	chr6:149637400-149640200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:149637400-149640400	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr6:149637400-149640400	Active TSS	Right Ventricle	heart
44	chr6:149637400-149640400	Active TSS	Hela-S3	cervix
45	chr6:149637400-149640600	Active TSS	NHDF-Ad	bronchial
46	chr6:149637400-149640800	Active TSS	H1 Cell Line	embryonic stem cell
47	chr6:149637400-149640800	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr6:149637400-149640800	Active TSS	Brain Cingulate Gyrus	brain
49	chr6:149637400-149640800	Active TSS	Fetal Stomach	stomach
50	chr6:149637400-149641000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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