Variant report

Variant	rs2329464
Chromosome Location	chr7:39710625-39710626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39617765..39620727-chr7:39709688..39712417,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11767632	0.96[CEU][hapmap]
rs11769865	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs11982634	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2107710	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2158548	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2158549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189837	0.93[EUR][1000 genomes]
rs2876862	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823742	0.93[EUR][1000 genomes]
rs4723887	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4723891	0.93[EUR][1000 genomes]
rs4723892	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462937	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs6952363	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6952866	0.89[EUR][1000 genomes]
rs6956681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961667	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6969070	0.89[EUR][1000 genomes]
rs6969523	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7785049	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7806651	0.84[EUR][1000 genomes]
rs917077	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2329464	LINC00265	cis	lung	GTEx
rs2329464	LINC00265	cis	Thyroid	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39672200-39722800	Weak transcription	Hela-S3	cervix
2	chr7:39680000-39721600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr7:39680800-39716400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr7:39682800-39722000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr7:39683400-39716600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr7:39683600-39712600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:39687400-39715000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr7:39692200-39714000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:39699400-39712000	Weak transcription	Fetal Kidney	kidney
10	chr7:39700000-39728200	Weak transcription	Liver	Liver
11	chr7:39701200-39718400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr7:39701800-39716400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr7:39701800-39720800	Weak transcription	Lung	lung
14	chr7:39701800-39721200	Weak transcription	Thymus	Thymus
15	chr7:39701800-39722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:39701800-39739400	Weak transcription	Esophagus	oesophagus
17	chr7:39702000-39716600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:39702000-39727400	Weak transcription	Fetal Intestine Large	intestine
19	chr7:39702200-39716400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr7:39703800-39711800	Weak transcription	GM12878-XiMat	blood
21	chr7:39703800-39716600	Weak transcription	Fetal Muscle Leg	muscle
22	chr7:39704000-39714600	Weak transcription	Primary T cells from cord blood	blood
23	chr7:39704200-39716400	Weak transcription	Fetal Intestine Small	intestine
24	chr7:39704200-39716600	Weak transcription	Psoas Muscle	Psoas
25	chr7:39704400-39711000	Weak transcription	NHEK	skin
26	chr7:39704400-39714800	Weak transcription	Primary B cells from cord blood	blood
27	chr7:39704400-39716200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr7:39704400-39717800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr7:39704800-39714600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr7:39704800-39718600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr7:39705200-39716200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:39706400-39710800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:39706400-39722800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr7:39706600-39716200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:39707200-39711400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr7:39707200-39711600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr7:39707200-39714200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:39707200-39714800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:39707200-39716000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:39707200-39727200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:39707200-39730000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr7:39707400-39714600	Weak transcription	Right Atrium	heart
43	chr7:39707400-39718400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr7:39707400-39718800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:39707400-39721000	Weak transcription	Right Ventricle	heart
46	chr7:39707600-39711200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:39707600-39711200	Weak transcription	HSMMtube	muscle
48	chr7:39707600-39711800	Weak transcription	Fetal Heart	heart
49	chr7:39707600-39711800	Weak transcription	NHLF	lung
50	chr7:39707600-39712600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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