Variant report

Variant	rs4729911
Chromosome Location	chr7:102976590-102976591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:102975707..102977886-chr7:102987978..102990881,2	MCF-7	breast:
2	chr7:102969608..102973527-chr7:102975201..102978233,5	K562	blood:
3	chr7:102975144..102978159-chr7:102980619..102982665,4	MCF-7	breast:
4	chr7:102965359..102966952-chr7:102976129..102978628,2	K562	blood:
5	chr7:102973791..102979614-chr7:102983161..102986751,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105821	Chromatin interaction
ENSG00000235354	Chromatin interaction
ENSG00000161057	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10245155	0.97[ASN][1000 genomes]
rs10266523	1.00[ASN][1000 genomes]
rs17606134	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs17680523	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1968201	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs2878	0.93[ASN][1000 genomes]
rs3087615	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35399723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5025411	0.92[CEU][hapmap]
rs62482370	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62482394	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482396	0.97[ASN][1000 genomes]
rs62482397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482398	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482403	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482404	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482406	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6971734	0.97[ASN][1000 genomes]
rs73175837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73175852	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7804020	0.92[CEU][hapmap]

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	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4729911	RP11-401L13.5	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102938600-102984200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:102939800-102980800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr7:102939800-102984000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:102939800-102984200	Weak transcription	Stomach Mucosa	stomach
5	chr7:102940000-102983000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:102948800-102982600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr7:102952000-102983800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:102954600-102984000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:102957400-102977000	Weak transcription	Fetal Brain Male	brain
10	chr7:102959400-102977000	Weak transcription	Colonic Mucosa	Colon
11	chr7:102959600-102981200	Weak transcription	Pancreas	Pancrea
12	chr7:102960200-102981000	Weak transcription	Fetal Heart	heart
13	chr7:102960400-102984200	Weak transcription	Spleen	Spleen
14	chr7:102960600-102977400	Weak transcription	Brain Angular Gyrus	brain
15	chr7:102960800-102977400	Weak transcription	Psoas Muscle	Psoas
16	chr7:102962400-102977200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:102962400-102977400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:102962400-102981400	Weak transcription	Gastric	stomach
19	chr7:102962400-102984200	Weak transcription	Aorta	Aorta
20	chr7:102963200-102977000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:102964800-102977200	Strong transcription	Fetal Intestine Small	intestine
22	chr7:102965600-102977200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr7:102965600-102977400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:102965800-102976800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr7:102965800-102977000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr7:102966000-102977400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:102966000-102981000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:102966400-102977400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:102966600-102977000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr7:102966800-102976800	Weak transcription	Brain Substantia Nigra	brain
31	chr7:102967000-102980800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr7:102967200-102976600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr7:102967600-102977400	Weak transcription	NHLF	lung
34	chr7:102967800-102977000	Weak transcription	HMEC	breast
35	chr7:102968000-102976600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr7:102968000-102977400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr7:102968000-102977600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr7:102969600-102977000	Weak transcription	NH-A	brain
39	chr7:102969800-102977000	Weak transcription	Primary B cells from cord blood	blood
40	chr7:102969800-102977400	Weak transcription	Brain Anterior Caudate	brain
41	chr7:102970800-102981600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:102970800-102982800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:102971200-102977200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:102971200-102980800	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr7:102971200-102983000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:102971400-102977400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr7:102971400-102981200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:102971400-102982400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr7:102971400-102982800	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr7:102971400-102983000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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