Variant report

Variant	rs6952363
Chromosome Location	chr7:39729140-39729141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39723283..39725435-chr7:39727516..39730400,2	MCF-7	breast:
2	chr7:39728943..39730510-chr7:39730672..39733182,2	K562	blood:
3	chr7:39723555..39727684-chr7:39728117..39732322,6	K562	blood:
4	chr7:39728709..39730955-chr7:39759969..39761928,2	K562	blood:

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11767632	0.96[CEU][hapmap];0.87[CHB][hapmap]
rs11769865	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11982634	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2107710	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2158548	0.89[EUR][1000 genomes]
rs2158549	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2189837	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237499	0.82[ASN][1000 genomes]
rs2329464	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2876862	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs3823742	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4723887	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4723891	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4723892	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6462936	0.83[EUR][1000 genomes]
rs6462937	0.87[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6952866	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6956681	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6961667	0.89[EUR][1000 genomes]
rs6969070	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6969523	0.92[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7785049	0.89[EUR][1000 genomes]
rs7806651	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs917077	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6952363	LINC00265	cis	Thyroid	GTEx
rs6952363	LINC00265	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39701800-39739400	Weak transcription	Esophagus	oesophagus
2	chr7:39707200-39730000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:39714000-39736800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:39715000-39736600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
6	chr7:39716800-39729200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr7:39716800-39735600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:39718200-39739800	Weak transcription	Spleen	Spleen
9	chr7:39721200-39730400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:39721200-39738200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:39721400-39730000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:39721400-39735800	Weak transcription	K562	blood
13	chr7:39721800-39736400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:39721800-39736600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:39722000-39737600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:39722800-39730000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr7:39722800-39738400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:39723000-39729200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:39723000-39731200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:39723200-39730000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr7:39723200-39730000	Weak transcription	Psoas Muscle	Psoas
22	chr7:39723200-39736000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:39723400-39729800	Weak transcription	Brain Germinal Matrix	brain
24	chr7:39723400-39736800	Weak transcription	Brain Hippocampus Middle	brain
25	chr7:39723600-39729800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:39723600-39730200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr7:39723600-39742800	Weak transcription	Brain Angular Gyrus	brain
28	chr7:39723800-39729800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr7:39723800-39730000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:39723800-39730000	Weak transcription	Fetal Kidney	kidney
31	chr7:39723800-39736200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr7:39723800-39737000	Weak transcription	Brain Anterior Caudate	brain
33	chr7:39723800-39743000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr7:39724000-39730000	Weak transcription	Fetal Brain Male	brain
35	chr7:39724000-39731400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr7:39724000-39739400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr7:39724200-39730000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr7:39724200-39736400	Weak transcription	Colonic Mucosa	Colon
39	chr7:39724200-39736600	Weak transcription	Colon Smooth Muscle	Colon
40	chr7:39724200-39741200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr7:39724600-39730000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr7:39724600-39739000	Weak transcription	Small Intestine	intestine
43	chr7:39725000-39732200	Weak transcription	Fetal Heart	heart
44	chr7:39725200-39730200	Weak transcription	Left Ventricle	heart
45	chr7:39725400-39732000	Genic enhancers	HUVEC	blood vessel
46	chr7:39726400-39729800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr7:39726400-39736800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:39726400-39737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr7:39726600-39733400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:39726600-39742800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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