Variant report

Variant	rs2246713
Chromosome Location	chr7:99802812-99802813
allele	C/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	chr7:99801934-99803494	K562	blood:	n/a	n/a
2	POLR2A	chr7:99802764-99803207	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr7:99802107-99802991	A549	lung:	n/a	n/a
4	POLR2A	chr7:99802766-99803095	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:99794786..99797012-chr7:99801296..99803017,2	K562	blood:
2	chr7:99797078..99799692-chr7:99801985..99803908,2	MCF-7	breast:
3	chr7:99753476..99755824-chr7:99801511..99804012,2	MCF-7	breast:

Variant related genes	Relation type
STAG3	TF binding region
ENSG00000266154	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000146826	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1043915	0.87[CHB][hapmap]
rs1061230	0.86[CHB][hapmap]
rs10953295	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1138417	0.86[CHB][hapmap]
rs11764176	0.86[CHB][hapmap]
rs12666425	0.87[CHB][hapmap]
rs12705073	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1623264	0.87[CHB][hapmap]
rs1624099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1636975	0.87[CHB][hapmap]
rs1637001	0.86[CHB][hapmap]
rs1727128	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727129	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1727133	0.86[CHB][hapmap]
rs1727134	0.87[CHB][hapmap]
rs1727138	0.86[CHB][hapmap]
rs1727140	0.87[CHB][hapmap]
rs1727143	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1727145	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859787	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2405442	0.82[CHB][hapmap]
rs2528900	0.87[CHB][hapmap]
rs2906646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950518	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2950520	0.86[CHB][hapmap]
rs3735241	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3735242	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3779045	0.87[CHB][hapmap]
rs4299940	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729580	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66809776	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6948729	0.86[CHB][hapmap]
rs705867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7794170	0.87[CHB][hapmap]
rs7799441	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7811662	0.87[CHB][hapmap]
rs858502	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs858506	0.86[CHB][hapmap]
rs858510	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs858513	0.87[CHB][hapmap]
rs866500	0.87[CHB][hapmap]
rs941287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
2	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
3	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
4	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
5	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv8182	chr7:99799816-99879781	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2246713	AP4M1	cis	Thyroid	GTEx
rs2246713	GATS	cis	multi-tissue	Pritchard
rs2246713	PVRIG	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99790000-99808800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr7:99790000-99817000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:99791400-99806800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:99793400-99806000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr7:99793600-99805800	Weak transcription	Primary T cells from cord blood	blood
6	chr7:99795600-99812200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:99795800-99807000	Weak transcription	Thymus	Thymus
8	chr7:99796000-99808400	Weak transcription	Brain Anterior Caudate	brain
9	chr7:99796400-99808800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:99796400-99813000	Weak transcription	Brain Substantia Nigra	brain
11	chr7:99796800-99816800	Weak transcription	Brain Germinal Matrix	brain
12	chr7:99796800-99817000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:99798000-99812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:99798200-99804800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:99798200-99806600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr7:99798200-99811200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:99798400-99806200	Weak transcription	Fetal Intestine Small	intestine
18	chr7:99798600-99806200	Weak transcription	Fetal Stomach	stomach
19	chr7:99798600-99810400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:99799000-99816600	Weak transcription	Fetal Brain Female	brain
21	chr7:99799200-99806200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:99799400-99806200	Weak transcription	Fetal Thymus	thymus
23	chr7:99799600-99808800	Weak transcription	Brain Hippocampus Middle	brain
24	chr7:99800200-99812000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr7:99801400-99826000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr7:99801600-99803000	Enhancers	Fetal Muscle Leg	muscle
27	chr7:99801600-99803200	Enhancers	Fetal Muscle Trunk	muscle
28	chr7:99802200-99803000	Strong transcription	Brain Cingulate Gyrus	brain
29	chr7:99802200-99803000	Strong transcription	Spleen	Spleen
30	chr7:99802200-99803200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:99802200-99806200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:99802400-99803000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr7:99802400-99803000	Strong transcription	Brain Angular Gyrus	brain
34	chr7:99802400-99803200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr7:99802400-99804800	Weak transcription	GM12878-XiMat	blood
36	chr7:99802600-99803000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:99802600-99803000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:99802600-99803000	Enhancers	Placenta	Placenta
39	chr7:99802600-99808400	Weak transcription	HSMMtube	muscle
40	chr7:99802800-99803000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:99802800-99803000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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