Variant report

Variant	rs3218651
Chromosome Location	chr3:121208176-121208177
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	chr3:121205844-121208503	K562	blood:	n/a	n/a

Variant related genes	Relation type
RPL7AP11	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11709797	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11717597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719937	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap]
rs1522357	0.89[ASW][hapmap]
rs16832303	0.92[CEU][hapmap]
rs3821367	1.00[ASW][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	nsv998555	chr3:120700604-121348015	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv829702	chr3:121045793-121227975	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv591400	chr3:121070299-121339354	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv877381	chr3:121192350-121343500	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1007522	chr3:121200563-121374051	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3218651	SEMA5B	cis	cerebellum	SCAN
rs3218651	LRRC58	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121151200-121263800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:121176400-121214800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:121176400-121224200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:121177200-121237000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:121177800-121214800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:121178000-121208600	Weak transcription	Fetal Heart	heart
7	chr3:121178200-121263800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:121181000-121219600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:121183800-121234400	Weak transcription	Primary B cells from cord blood	blood
10	chr3:121186400-121255600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:121186600-121211600	Weak transcription	Primary T cells from cord blood	blood
12	chr3:121186800-121213000	Weak transcription	Fetal Intestine Small	intestine
13	chr3:121187000-121209600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:121187200-121223400	Weak transcription	Fetal Intestine Large	intestine
15	chr3:121192200-121233600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:121193000-121212400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:121193200-121237000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:121195200-121208200	Weak transcription	Thymus	Thymus
19	chr3:121195600-121233800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:121196000-121208800	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:121196800-121208600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:121197200-121217400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:121197200-121233400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:121198800-121210000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:121199200-121216200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:121199800-121213200	Weak transcription	Fetal Stomach	stomach
27	chr3:121200400-121222000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:121200600-121264000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:121201000-121209000	Weak transcription	Hela-S3	cervix
30	chr3:121201000-121227000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:121201000-121250600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:121202000-121208200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:121202000-121208400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:121202000-121208800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:121202400-121209000	Weak transcription	HUVEC	blood vessel
36	chr3:121202400-121215600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:121202400-121263200	Weak transcription	NHLF	lung
38	chr3:121202400-121263800	Weak transcription	HSMM	muscle
39	chr3:121202600-121208600	Weak transcription	NHDF-Ad	bronchial
40	chr3:121202600-121209600	Weak transcription	Osteobl	bone
41	chr3:121202600-121214400	Weak transcription	NH-A	brain
42	chr3:121202600-121233400	Weak transcription	NHEK	skin
43	chr3:121202800-121236600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr3:121203600-121208600	Weak transcription	GM12878-XiMat	blood
45	chr3:121206000-121213200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:121206000-121217800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:121206200-121210000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:121206200-121213400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:121206200-121216200	Strong transcription	Dnd41	blood
50	chr3:121206200-121216800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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