Variant report

Variant	rs517237
Chromosome Location	chr1:120284988-120284989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120278740..120281495-chr1:120284812..120287109,2	MCF-7	breast:
2	chr1:120282346..120286075-chr1:120287322..120291391,4	K562	blood:
3	chr1:120278363..120280873-chr1:120284153..120287954,3	K562	blood:
4	chr1:120283662..120285685-chr1:120414247..120416692,2	MCF-7	breast:
5	chr1:120281250..120283814-chr1:120284593..120287866,3	K562	blood:

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1441009	0.92[CEU][hapmap]
rs1441010	0.83[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs2843019	0.83[AMR][1000 genomes]
rs522277	0.82[CHD][hapmap]
rs532208	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs536662	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs543703	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs591162	0.82[CHD][hapmap]
rs593911	0.82[CHD][hapmap]
rs596104	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs609558	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610404	0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs619167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs627070	0.81[ASN][1000 genomes]
rs662924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs673816	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs689198	0.82[CHB][hapmap];0.85[JPT][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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
7	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs517237	NBPF7	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120257200-120287000	Weak transcription	NH-A	brain
2	chr1:120258600-120289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:120260400-120287600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:120261000-120287200	Strong transcription	Hela-S3	cervix
5	chr1:120261600-120288200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:120261800-120287000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:120261800-120287600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:120262000-120287200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:120262000-120287400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:120262000-120287400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:120262000-120287800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:120262000-120288200	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr1:120262400-120285000	Strong transcription	NHEK	skin
14	chr1:120262400-120287400	Strong transcription	Dnd41	blood
15	chr1:120262400-120288200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:120263200-120286400	Strong transcription	Thymus	Thymus
17	chr1:120263400-120286800	Strong transcription	Primary T cells from cord blood	blood
18	chr1:120263400-120287400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:120263400-120291400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:120267200-120286800	Weak transcription	Primary B cells from cord blood	blood
21	chr1:120269800-120286800	Weak transcription	Small Intestine	intestine
22	chr1:120271000-120286600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:120271200-120286200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:120272800-120285200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:120274000-120286400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:120275200-120286800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:120275600-120285000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:120275800-120286200	Strong transcription	HepG2	liver
29	chr1:120276400-120285200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:120276400-120285800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:120278600-120287000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:120279200-120286600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr1:120279200-120290600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr1:120280200-120286600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:120280400-120285000	Weak transcription	Esophagus	oesophagus
36	chr1:120280400-120285000	Strong transcription	Placenta	Placenta
37	chr1:120280400-120286000	Weak transcription	Fetal Brain Female	brain
38	chr1:120280400-120286400	Weak transcription	Colonic Mucosa	Colon
39	chr1:120280400-120289400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:120280600-120286400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:120280600-120286800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:120280800-120287000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:120281000-120285000	Weak transcription	Brain Anterior Caudate	brain
44	chr1:120281000-120285200	Strong transcription	Fetal Intestine Large	intestine
45	chr1:120281000-120286200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:120281200-120285000	Weak transcription	Brain Substantia Nigra	brain
47	chr1:120281200-120285200	Strong transcription	Fetal Intestine Small	intestine
48	chr1:120281200-120285400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:120281200-120285800	Weak transcription	Stomach Mucosa	stomach
50	chr1:120281200-120287000	Weak transcription	K562	blood

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