Variant report

Variant	rs6717139
Chromosome Location	chr2:20116284-20116285
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20100607..20103540-chr2:20114213..20116931,4	K562	blood:
2	chr2:20110141..20113047-chr2:20115173..20117476,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271991	Chromatin interaction
ENSG00000183891	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10175236	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175486	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10190645	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10203067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10211513	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096633	0.94[CEU][hapmap]
rs1147110	0.89[CEU][hapmap]
rs11887799	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12328613	0.94[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12467740	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478941	1.00[CEU][hapmap]
rs12615824	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1462754	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16987206	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16987297	1.00[CEU][hapmap]
rs2278528	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304589	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28742930	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3754907	0.82[CEU][hapmap]
rs3754908	0.82[CEU][hapmap]
rs3769763	0.83[CEU][hapmap]
rs58978345	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6716854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721754	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6757734	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
4	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv527453	chr2:20109061-20160209	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6717139	TTC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102400-20126600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:20102600-20119000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:20102600-20127600	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:20102600-20127800	Weak transcription	Aorta	Aorta
5	chr2:20102600-20128000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:20102800-20123200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:20102800-20123600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:20102800-20126600	Weak transcription	Adipose Nuclei	Adipose
9	chr2:20102800-20126600	Weak transcription	Fetal Lung	lung
10	chr2:20102800-20126800	Weak transcription	Fetal Kidney	kidney
11	chr2:20102800-20127200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:20102800-20127600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:20102800-20127600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:20102800-20128800	Weak transcription	Liver	Liver
15	chr2:20102800-20128800	Weak transcription	Brain Germinal Matrix	brain
16	chr2:20102800-20129000	Weak transcription	Brain Anterior Caudate	brain
17	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
18	chr2:20103000-20126800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:20103000-20127400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:20105000-20127400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:20105400-20129000	Weak transcription	Primary T cells from cord blood	blood
22	chr2:20105400-20130200	Weak transcription	Lung	lung
23	chr2:20106600-20117400	Weak transcription	GM12878-XiMat	blood
24	chr2:20107800-20123400	Weak transcription	Left Ventricle	heart
25	chr2:20108600-20127400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:20108800-20137400	Weak transcription	Right Ventricle	heart
27	chr2:20109200-20126600	Weak transcription	Primary B cells from cord blood	blood
28	chr2:20110800-20117600	Weak transcription	Pancreas	Pancrea
29	chr2:20111000-20126600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:20111800-20127800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:20112200-20128400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:20112200-20130000	Weak transcription	HSMMtube	muscle
33	chr2:20112400-20123200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:20112400-20126600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:20112400-20126800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:20112400-20128000	Weak transcription	Osteobl	bone
37	chr2:20112400-20128400	Weak transcription	NHDF-Ad	bronchial
38	chr2:20112600-20126800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:20112600-20126800	Weak transcription	HMEC	breast
40	chr2:20112600-20128800	Weak transcription	Hela-S3	cervix
41	chr2:20114000-20126200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:20114000-20126200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:20114000-20129000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:20114200-20123200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:20114200-20124200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:20114200-20128200	Weak transcription	HepG2	liver
47	chr2:20114400-20122600	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:20114400-20122800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:20114400-20124400	Weak transcription	HUVEC	blood vessel
50	chr2:20114400-20126800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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