Variant report

Variant	rs734538
Chromosome Location	chr6:35205881-35205882
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35195154..35200305-chr6:35202213..35207133,5	K562	blood:
2	chr6:35132640..35135454-chr6:35205817..35208602,3	MCF-7	breast:
3	chr6:35173439..35175719-chr6:35204862..35206490,2	K562	blood:
4	chr6:34760038..34762450-chr6:35204039..35206411,2	K562	blood:
5	chr6:35196327..35198090-chr6:35203601..35206096,2	MCF-7	breast:
6	chr6:35188260..35190147-chr6:35205667..35207207,2	K562	blood:
7	chr6:35202209..35206634-chr6:35208195..35211678,7	K562	blood:
8	chr6:35203262..35205063-chr6:35205452..35207429,2	K562	blood:
9	chr6:35205769..35207687-chr6:35225072..35226945,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000065029	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11552398	1.00[GIH][hapmap]
rs13216424	0.88[GIH][hapmap]
rs16871749	1.00[GIH][hapmap]
rs16871814	1.00[GIH][hapmap]
rs1929846	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929848	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234044	1.00[GIH][hapmap]
rs2395617	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756856	1.00[GIH][hapmap];0.83[MKK][hapmap]
rs4713842	1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs4713843	1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs4713844	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713846	0.81[EUR][1000 genomes]
rs6457815	1.00[CHB][hapmap]
rs6906666	1.00[GIH][hapmap]
rs6919534	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931442	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707969	0.82[MEX][hapmap]
rs729925	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763155	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763157	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751726	1.00[CHB][hapmap]
rs7767150	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770619	1.00[CHB][hapmap]
rs820062	0.88[GIH][hapmap]
rs820065	0.88[GIH][hapmap]
rs820069	0.88[GIH][hapmap]
rs820095	1.00[GIH][hapmap]
rs820099	0.88[GIH][hapmap]
rs820101	0.88[GIH][hapmap]
rs9394282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462081	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9658077	1.00[CHB][hapmap]
rs9658081	1.00[CHB][hapmap]
rs9658085	1.00[CHB][hapmap]
rs9658089	1.00[CHD][hapmap]
rs9658118	1.00[CHD][hapmap]
rs9658119	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9658136	1.00[CHD][hapmap]
rs9658151	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3428128	chr6:35150524-35225843	Bivalent Enhancer Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs734538	TPM2	trans	lymphoblastoid	seeQTL
rs734538	TCP11	cis	lymphoblastoid	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35182400-35209000	Weak transcription	A549	lung
2	chr6:35186400-35212000	Weak transcription	NHDF-Ad	bronchial
3	chr6:35186800-35212000	Weak transcription	Dnd41	blood
4	chr6:35188200-35206400	Weak transcription	NH-A	brain
5	chr6:35190200-35212000	Weak transcription	Brain Angular Gyrus	brain
6	chr6:35191200-35212000	Weak transcription	Primary T cells from cord blood	blood
7	chr6:35191400-35226000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:35192200-35211400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:35194000-35209400	Weak transcription	Thymus	Thymus
10	chr6:35194000-35225600	Weak transcription	Primary B cells from cord blood	blood
11	chr6:35195600-35210600	Weak transcription	Spleen	Spleen
12	chr6:35199200-35211800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:35199200-35212200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:35199400-35208800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:35199400-35209200	Weak transcription	Adipose Nuclei	Adipose
16	chr6:35199400-35211800	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:35199400-35212000	Weak transcription	Brain Anterior Caudate	brain
18	chr6:35199400-35216200	Weak transcription	Brain Substantia Nigra	brain
19	chr6:35199600-35209800	Weak transcription	Gastric	stomach
20	chr6:35199600-35210400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:35199600-35211200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:35199600-35215600	Weak transcription	Hela-S3	cervix
23	chr6:35199600-35226600	Weak transcription	Esophagus	oesophagus
24	chr6:35199800-35206200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:35199800-35206800	Weak transcription	Ovary	ovary
26	chr6:35199800-35212200	Weak transcription	HepG2	liver
27	chr6:35199800-35226200	Weak transcription	Pancreas	Pancrea
28	chr6:35200000-35206000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:35200600-35225000	Weak transcription	Fetal Brain Male	brain
30	chr6:35201400-35226200	Weak transcription	Stomach Mucosa	stomach
31	chr6:35201600-35211800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:35202600-35206200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:35202600-35225800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:35203400-35206000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:35203400-35226000	Weak transcription	HSMMtube	muscle
36	chr6:35203600-35210600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:35204000-35207000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:35204000-35208400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
39	chr6:35204000-35209000	Enhancers	Left Ventricle	heart
40	chr6:35204200-35206000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
41	chr6:35204200-35206600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:35204200-35208400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
43	chr6:35204400-35206000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:35204400-35207400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:35204400-35215400	Weak transcription	GM12878-XiMat	blood
46	chr6:35204600-35206600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:35204600-35207400	Enhancers	Placenta Amnion	Placenta Amnion
48	chr6:35204600-35207800	Weak transcription	NHEK	skin
49	chr6:35204600-35208000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
50	chr6:35204600-35208600	Genic enhancers	Fetal Stomach	stomach

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