Variant report

Variant	rs2071387
Chromosome Location	chr3:139257603-139257604
allele	C/T
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	MXI1	chr3:139254870-139260531	SK-N-SH	brain:	n/a	n/a
2	FOSL1	chr3:139255939-139257885	HCT-116	colon:	n/a	chr3:139256357-139256365 chr3:139256358-139256365 chr3:139256356-139256366 chr3:139256355-139256367 chr3:139256357-139256366 chr3:139256356-139256365 chr3:139257128-139257140
3	JUND	chr3:139255655-139257823	SK-N-SH	brain:	n/a	chr3:139256357-139256365 chr3:139256355-139256366 chr3:139256358-139256365 chr3:139256356-139256366 chr3:139256355-139256367 chr3:139256357-139256366 chr3:139256356-139256365 chr3:139257128-139257140
4	NFYB	chr3:139257565-139257684	GM12878	blood:	n/a	n/a
5	EP300	chr3:139251629-139259175	SK-N-SH	brain:	n/a	chr3:139256357-139256366 chr3:139253631-139253641 chr3:139252024-139252040 chr3:139256356-139256365
6	MXI1	chr3:139257591-139257791	H1-hESC	embryonic stem cell:	n/a	n/a
7	SIN3AK20	chr3:139256022-139258994	HCT-116	colon:	n/a	n/a
8	TCF7L2	chr3:139256709-139257982	HCT-116	colon:	n/a	chr3:139257148-139257157 chr3:139257147-139257156 chr3:139256975-139256989 chr3:139257144-139257160 chr3:139256977-139256986 chr3:139257149-139257156 chr3:139257144-139257160
9	CEBPB	chr3:139257603-139257922	IMR90	lung:	n/a	n/a
10	JUND	chr3:139256007-139258019	HCT-116	colon:	n/a	chr3:139256357-139256365 chr3:139256355-139256366 chr3:139256358-139256365 chr3:139256356-139256366 chr3:139256355-139256367 chr3:139256357-139256366 chr3:139256356-139256365 chr3:139257128-139257140
11	CBX3	chr3:139256018-139258020	HCT-116	colon:	n/a	n/a
12	JUND	chr3:139255896-139258067	HCT-116	colon:	n/a	chr3:139256357-139256365 chr3:139256355-139256366 chr3:139256358-139256365 chr3:139256356-139256366 chr3:139256355-139256367 chr3:139256357-139256366 chr3:139256356-139256365 chr3:139257128-139257140
13	POLR2A	chr3:139256775-139258093	HCT-116	colon:	n/a	n/a
14	SP1	chr3:139255938-139258057	HCT-116	colon:	n/a	chr3:139256874-139256887
15	SP1	chr3:139255901-139258032	HCT-116	colon:	n/a	chr3:139256874-139256887

Variant related genes	Relation type
ENSG00000248932	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10935331	0.81[CHB][hapmap]
rs12485273	0.82[ASW][hapmap];0.87[CEU][hapmap];0.88[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2071387	RBP1	cis	parietal	SCAN
rs2071387	RBP1	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139251800-139258600	Enhancers	Fetal Heart	heart
2	chr3:139252800-139257800	Weak transcription	Psoas Muscle	Psoas
3	chr3:139253000-139258000	Weak transcription	Small Intestine	intestine
4	chr3:139253000-139258200	Enhancers	Spleen	Spleen
5	chr3:139255000-139257800	Weak transcription	HSMM	muscle
6	chr3:139255000-139258000	Weak transcription	NHLF	lung
7	chr3:139255000-139258200	Weak transcription	Gastric	stomach
8	chr3:139255200-139258000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:139255400-139257800	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:139256200-139257800	Weak transcription	Aorta	Aorta
11	chr3:139256200-139257800	Flanking Active TSS	Pancreas	Pancrea
12	chr3:139256200-139258000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:139256200-139258000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:139256400-139257800	ZNF genes & repeats	HMEC	breast
15	chr3:139256400-139258000	ZNF genes & repeats	NHEK	skin
16	chr3:139256600-139257800	Bivalent Enhancer	Placenta	Placenta
17	chr3:139256600-139257800	Enhancers	Right Atrium	heart
18	chr3:139256800-139257800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:139256800-139257800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:139256800-139258200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:139257200-139257800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
22	chr3:139257200-139257800	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr3:139257200-139257800	Transcr. at gene 5' and 3'	HSMMtube	muscle
24	chr3:139257200-139258400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr3:139257400-139257800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
26	chr3:139257400-139257800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
27	chr3:139257400-139257800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
28	chr3:139257400-139257800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:139257400-139257800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr3:139257400-139257800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:139257400-139257800	Active TSS	Brain Germinal Matrix	brain
32	chr3:139257400-139257800	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr3:139257400-139257800	Enhancers	Esophagus	oesophagus
34	chr3:139257400-139257800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
35	chr3:139257400-139257800	Flanking Active TSS	Fetal Intestine Large	intestine
36	chr3:139257400-139257800	Enhancers	Lung	lung
37	chr3:139257400-139257800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
38	chr3:139257400-139257800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
39	chr3:139257400-139257800	Flanking Active TSS	NH-A	brain
40	chr3:139257400-139258000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
41	chr3:139257400-139258000	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr3:139257400-139258000	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr3:139257400-139258000	Flanking Active TSS	Fetal Stomach	stomach
44	chr3:139257400-139258200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
45	chr3:139257400-139258200	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr3:139257400-139259400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr3:139257600-139257800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:139257600-139257800	Flanking Bivalent TSS/Enh	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:139257600-139257800	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
50	chr3:139257600-139257800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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