Variant report

Variant	rs2598304
Chromosome Location	chr7:32982027-32982028
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:61582496..61583159-chr7:32981810..32982571,2	Hela-S3	cervix:
2	chr4:15003964..15004491-chr7:32981733..32982311,2	Hela-S3	cervix:
3	chr7:32981289..32983857-chr7:33147743..33149971,3	K562	blood:
4	chr7:32917579..32920206-chr7:32981301..32983745,3	K562	blood:
5	chr7:32981284..32982799-chr7:33074781..33076751,2	MCF-7	breast:
6	chr7:32929776..32933176-chr7:32979221..32984586,9	K562	blood:
7	chr7:32804013..32805676-chr7:32980838..32982358,2	K562	blood:
8	chr7:32981007..32984575-chr7:32996149..32999305,3	K562	blood:
9	chr7:32981269..32984259-chr7:33078718..33080736,2	K562	blood:
10	chr7:32929776..32933604-chr7:32979221..32983668,8	K562	blood:
11	chr7:32979720..32982452-chr7:32995227..32996993,2	MCF-7	breast:
12	chr7:32981117..32983868-chr7:33100044..33104533,5	K562	blood:
13	chr7:32930144..32933103-chr7:32981604..32984201,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KBTBD2-2	chr7:32981932-32982159	NONHSAT120007

No data

Variant related genes	Relation type
ENSG00000122642	Chromatin interaction
ENSG00000149485	Chromatin interaction
ENSG00000229054	Chromatin interaction
ENSG00000170852	Chromatin interaction
ENSG00000222326	Chromatin interaction
ENSG00000164610	Chromatin interaction
ENSG00000137449	Chromatin interaction
ENSG00000122643	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11771075	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13247369	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13311608	0.84[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs13437980	0.86[ASN][1000 genomes]
rs17356044	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465899	0.87[ASN][1000 genomes]
rs34556400	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3750076	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3750077	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3750079	0.81[CEU][hapmap]
rs4723224	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6970641	0.88[ASN][1000 genomes]
rs6970869	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784449	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7786644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7787304	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7787645	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7790246	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];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7806466	0.84[ASN][1000 genomes]
rs7808290	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];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7809397	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv1029220	chr7:32921484-33262190	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	esv3478254	chr7:32956181-33133477	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	esv3478255	chr7:32956181-33133477	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv3528603	chr7:32956254-33133429	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	esv3528604	chr7:32956254-33133429	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	esv3366191	chr7:32956659-33134592	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1033096	chr7:32965040-33039206	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	esv3418466	chr7:32968130-33138898	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	esv3356222	chr7:32980952-32983800	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2598304	NPSR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:32980600-32983000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr7:32980600-32983200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:32980600-32983200	Active TSS	NHLF	lung
4	chr7:32980600-32983600	Active TSS	NHDF-Ad	bronchial
5	chr7:32980800-32982200	Active TSS	Fetal Brain Male	brain
6	chr7:32980800-32982600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:32980800-32982800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:32980800-32983000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:32980800-32983000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:32980800-32983000	Active TSS	Fetal Brain Female	brain
11	chr7:32980800-32983000	Active TSS	Right Atrium	heart
12	chr7:32980800-32983000	Active TSS	NHEK	skin
13	chr7:32980800-32983200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:32980800-32983200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:32980800-32983200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:32980800-32983200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr7:32980800-32983200	Active TSS	HSMMtube	muscle
18	chr7:32980800-32983400	Active TSS	Brain Germinal Matrix	brain
19	chr7:32981000-32982600	Active TSS	Fetal Intestine Large	intestine
20	chr7:32981000-32982800	Active TSS	Aorta	Aorta
21	chr7:32981000-32982800	Active TSS	Fetal Intestine Small	intestine
22	chr7:32981000-32983000	Active TSS	Right Ventricle	heart
23	chr7:32981200-32982200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr7:32981200-32982800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr7:32981200-32982800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr7:32981200-32983000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:32981200-32983000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:32981200-32983000	Active TSS	Left Ventricle	heart
29	chr7:32981200-32983000	Active TSS	Psoas Muscle	Psoas
30	chr7:32981200-32983200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:32981200-32983200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:32981200-32983200	Active TSS	Brain Cingulate Gyrus	brain
33	chr7:32981200-32983200	Active TSS	Fetal Muscle Trunk	muscle
34	chr7:32981200-32983200	Active TSS	Ovary	ovary
35	chr7:32981200-32983200	Active TSS	HSMM	muscle
36	chr7:32981200-32983400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr7:32981400-32982400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr7:32981400-32982400	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr7:32981400-32982600	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr7:32981400-32982800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:32981400-32982800	Active TSS	Esophagus	oesophagus
42	chr7:32981400-32982800	Active TSS	Pancreas	Pancrea
43	chr7:32981400-32982800	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr7:32981400-32982800	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr7:32981400-32982800	Active TSS	HMEC	breast
46	chr7:32981400-32982800	Active TSS	K562	blood
47	chr7:32981400-32983000	Active TSS	Muscle Satellite Cultured Cells	--
48	chr7:32981400-32983000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:32981400-32983000	Active TSS	Colon Smooth Muscle	Colon
50	chr7:32981400-32983000	Active TSS	Duodenum Smooth Muscle	Duodenum

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