Variant report

Variant	rs6956681
Chromosome Location	chr7:39733688-39733689
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39729170..39731392-chr7:39733307..39735068,2	K562	blood:
2	chr7:39729892..39732423-chr7:39733568..39735787,2	K562	blood:
3	chr7:39661332..39663000-chr7:39732479..39734683,2	K562	blood:
4	chr7:39732340..39735300-chr7:39760265..39762340,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11767632	0.95[CEU][hapmap]
rs11769865	0.95[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs11982634	0.95[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2107710	0.95[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs2158548	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2158549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189837	0.93[EUR][1000 genomes]
rs2329464	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]
rs2876862	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823742	0.93[EUR][1000 genomes]
rs4723887	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4723891	0.93[EUR][1000 genomes]
rs4723892	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462937	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs6952363	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6952866	0.89[EUR][1000 genomes]
rs6961667	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6969070	0.89[EUR][1000 genomes]
rs6969523	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs7785049	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7806651	0.84[EUR][1000 genomes]
rs917077	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6956681	LINC00265	cis	Thyroid	GTEx
rs6956681	HECW1	cis	parietal	SCAN
rs6956681	RALA	cis	cerebellum	SCAN
rs6956681	C7orf11	cis	cerebellum	SCAN
rs6956681	LINC00265	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39701800-39739400	Weak transcription	Esophagus	oesophagus
2	chr7:39714000-39736800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:39715000-39736600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
5	chr7:39716800-39735600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:39718200-39739800	Weak transcription	Spleen	Spleen
7	chr7:39721200-39738200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr7:39721400-39735800	Weak transcription	K562	blood
9	chr7:39721800-39736400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:39721800-39736600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:39722000-39737600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:39722800-39738400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:39723200-39736000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:39723400-39736800	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:39723600-39742800	Weak transcription	Brain Angular Gyrus	brain
16	chr7:39723800-39736200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:39723800-39737000	Weak transcription	Brain Anterior Caudate	brain
18	chr7:39723800-39743000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:39724000-39739400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:39724200-39736400	Weak transcription	Colonic Mucosa	Colon
21	chr7:39724200-39736600	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:39724200-39741200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr7:39724600-39739000	Weak transcription	Small Intestine	intestine
24	chr7:39726400-39736800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:39726400-39737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:39726600-39742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr7:39727000-39734200	Strong transcription	Primary T cells from cord blood	blood
28	chr7:39727000-39738000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:39727200-39733800	Strong transcription	Primary B cells from peripheral blood	blood
30	chr7:39727400-39741600	Strong transcription	Fetal Muscle Leg	muscle
31	chr7:39727400-39747800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:39727600-39734400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr7:39727600-39734600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr7:39727600-39741200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr7:39728200-39733800	Strong transcription	Fetal Muscle Trunk	muscle
36	chr7:39728600-39736400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr7:39728800-39736800	Weak transcription	Gastric	stomach
38	chr7:39728800-39736800	Weak transcription	Lung	lung
39	chr7:39728800-39737000	Weak transcription	Right Ventricle	heart
40	chr7:39728800-39739800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:39729000-39736400	Weak transcription	Thymus	Thymus
42	chr7:39729000-39736600	Weak transcription	A549	lung
43	chr7:39729000-39739400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:39729000-39742400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr7:39729200-39733800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr7:39729200-39735600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr7:39729400-39736000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr7:39729400-39739000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:39729400-39740000	Weak transcription	Stomach Mucosa	stomach
50	chr7:39729600-39734400	Weak transcription	Fetal Intestine Small	intestine

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