Variant report

Variant	rs6952407
Chromosome Location	chr7:66045512-66045513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:66045352-66045656	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:66045322-66045575	K562	blood:	n/a	n/a
3	POLR2A	chr7:66045189-66045703	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:66044739..66046624-chr7:66048819..66050510,2	K562	blood:
2	chr7:66039081..66041475-chr7:66044716..66046904,2	K562	blood:
3	chr7:66044695..66047717-chr7:66050273..66053007,3	K562	blood:

Variant related genes	Relation type
ENSG00000232559	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10234018	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs10249404	0.96[CEU][hapmap];0.96[YRI][hapmap]
rs10252765	0.96[CEU][hapmap];0.95[YRI][hapmap]
rs10263935	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs10950044	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs12532998	0.91[YRI][hapmap]
rs13227951	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1553610	0.95[YRI][hapmap]
rs1968225	0.92[YRI][hapmap]
rs2013222	0.96[CEU][hapmap]
rs2077593	0.84[YRI][hapmap]
rs2191268	0.96[CEU][hapmap];0.96[YRI][hapmap]
rs2244022	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs2286683	0.96[CEU][hapmap]
rs2302918	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs2707845	0.93[CEU][hapmap];0.96[YRI][hapmap]
rs2707852	0.88[YRI][hapmap]
rs2707853	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs2707854	0.96[CEU][hapmap];0.95[YRI][hapmap]
rs2707856	0.96[CEU][hapmap];0.95[YRI][hapmap]
rs3735148	0.90[YRI][hapmap]
rs3764903	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs3800812	0.96[CEU][hapmap];0.96[YRI][hapmap]
rs3800820	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs6460296	0.88[YRI][hapmap]
rs6460305	0.96[CEU][hapmap];0.95[YRI][hapmap]
rs6460308	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs6943696	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs6945019	0.92[YRI][hapmap]
rs6945032	0.91[YRI][hapmap]
rs6947808	0.87[YRI][hapmap]
rs6958520	0.96[CEU][hapmap];0.95[YRI][hapmap]
rs7789768	0.91[YRI][hapmap]
rs7793569	0.96[CEU][hapmap];0.96[YRI][hapmap]
rs801205	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs801217	0.96[CEU][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv3377926	chr7:65934493-66051484	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	esv3423847	chr7:65941210-66054107	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv970868	chr7:66035219-66056610	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Cotinine glucuronidation	25293881	GWAS catalog

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6952407	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6952407	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6952407	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs6952407	RP4-756H11.3	cis	Thyroid	GTEx
rs6952407	RP4-756H11.3	cis	lung	GTEx
rs6952407	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6952407	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6952407	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6952407	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6952407	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs6952407	RP4-756H11.3	cis	Stomach	GTEx
rs6952407	RP4-756H11.3	cis	Artery Aorta	GTEx
rs6952407	RP4-756H11.3	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66004400-66052600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:66008600-66056000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:66021800-66056400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:66023200-66048400	Weak transcription	Colon Smooth Muscle	Colon
5	chr7:66023200-66049800	Weak transcription	Stomach Mucosa	stomach
6	chr7:66023200-66055400	Weak transcription	Fetal Brain Male	brain
7	chr7:66024000-66046400	Weak transcription	NHLF	lung
8	chr7:66024200-66051200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:66024200-66055400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:66024200-66055600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:66024400-66051600	Weak transcription	Spleen	Spleen
12	chr7:66029400-66046200	Weak transcription	Pancreas	Pancrea
13	chr7:66034800-66046400	Weak transcription	A549	lung
14	chr7:66037600-66056400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:66037800-66051200	Weak transcription	Small Intestine	intestine
16	chr7:66037800-66054800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:66038000-66052400	Weak transcription	Psoas Muscle	Psoas
18	chr7:66038000-66056200	Weak transcription	Colonic Mucosa	Colon
19	chr7:66038200-66048400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:66038200-66048600	Weak transcription	Brain Germinal Matrix	brain
21	chr7:66038200-66055400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr7:66038200-66055800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr7:66038400-66055400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr7:66038800-66055400	Weak transcription	Fetal Lung	lung
25	chr7:66039200-66054600	Weak transcription	Fetal Brain Female	brain
26	chr7:66039400-66046200	Weak transcription	Gastric	stomach
27	chr7:66039400-66051200	Weak transcription	Ovary	ovary
28	chr7:66039400-66054200	Weak transcription	Right Ventricle	heart
29	chr7:66039400-66054200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:66039400-66055400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr7:66039400-66055400	Weak transcription	Fetal Kidney	kidney
32	chr7:66039400-66055400	Weak transcription	HUVEC	blood vessel
33	chr7:66039400-66055400	Weak transcription	NH-A	brain
34	chr7:66039600-66048600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr7:66039600-66054800	Weak transcription	Esophagus	oesophagus
36	chr7:66039800-66055400	Weak transcription	HSMMtube	muscle
37	chr7:66040000-66047200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr7:66040000-66048400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:66040000-66051600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr7:66040200-66046200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:66040200-66048400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr7:66040200-66056200	Weak transcription	Aorta	Aorta
43	chr7:66040400-66051600	Weak transcription	Lung	lung
44	chr7:66040800-66046200	Weak transcription	Liver	Liver
45	chr7:66041000-66048200	Weak transcription	Fetal Thymus	thymus
46	chr7:66041400-66051800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr7:66041800-66046000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr7:66041800-66046200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr7:66041800-66046200	Weak transcription	Adipose Nuclei	Adipose
50	chr7:66041800-66046400	Weak transcription	Stomach Smooth Muscle	stomach

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