Variant report

Variant	rs2071486
Chromosome Location	chr4:122740162-122740163
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:122729816..122733946-chr4:122739910..122742297,4	MCF-7	breast:
2	chr4:122736991..122740974-chr4:122741113..122746260,6	MCF-7	breast:
3	chr4:122738481..122743178-chr4:122755904..122760615,4	K562	blood:

Variant related genes	Relation type
ENSG00000123737	Chromatin interaction
ENSG00000145386	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11098645	0.91[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11098646	0.91[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11098648	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11731570	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11731917	0.91[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12512876	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1396080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507994	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1507995	0.83[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17452156	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2063165	0.89[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2221628	0.91[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3217753	0.91[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3217771	0.91[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3217773	0.91[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3217780	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3828485	0.84[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3924987	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4077102	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4516739	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56077950	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56159666	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56311153	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58649165	0.83[EUR][1000 genomes]
rs61217486	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6534323	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67772833	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6815790	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6821305	0.99[ASN][1000 genomes]
rs6823818	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6826506	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6838153	0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6855269	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72680779	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7660548	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7672640	0.85[LWK][hapmap];0.92[YRI][hapmap]
rs7686084	0.91[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7686200	0.91[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7691955	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs769238	0.91[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs769246	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7699776	0.91[CEU][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9684587	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer 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 miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2071486	BBS7	cis	parietal	SCAN
rs2071486	BBS7	cis	cerebellum	SCAN
rs2071486	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122723000-122743600	Weak transcription	Esophagus	oesophagus
2	chr4:122723000-122743600	Weak transcription	Small Intestine	intestine
3	chr4:122723000-122744200	Weak transcription	Gastric	stomach
4	chr4:122723000-122744600	Weak transcription	Aorta	Aorta
5	chr4:122723200-122741800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:122723200-122743400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:122723200-122743600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:122723200-122743800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:122723400-122744200	Weak transcription	Stomach Mucosa	stomach
10	chr4:122723600-122742200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:122723600-122742400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:122723600-122742800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:122723800-122740400	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:122723800-122740400	Strong transcription	Fetal Intestine Large	intestine
15	chr4:122723800-122740600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:122723800-122741800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr4:122723800-122742200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:122723800-122742400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:122723800-122743000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:122723800-122743000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:122723800-122743000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:122724000-122740200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:122724000-122740400	Strong transcription	Placenta	Placenta
24	chr4:122724000-122740400	Strong transcription	NH-A	brain
25	chr4:122724000-122741800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr4:122724000-122742600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:122724000-122743400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr4:122724200-122740200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:122724200-122740400	Strong transcription	Stomach Smooth Muscle	stomach
30	chr4:122724200-122741000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr4:122724200-122741200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:122724200-122742800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:122724400-122741000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr4:122724400-122742200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:122724400-122742600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr4:122724400-122744000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr4:122724600-122742000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:122725200-122740200	Strong transcription	Adipose Nuclei	Adipose
39	chr4:122725200-122741800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:122725400-122742600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:122725400-122742600	Strong transcription	Fetal Thymus	thymus
42	chr4:122725600-122740400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:122725800-122740600	Strong transcription	Brain Hippocampus Middle	brain
44	chr4:122726400-122740200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:122727600-122741800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr4:122729600-122740200	Weak transcription	NHLF	lung
47	chr4:122730200-122744000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:122730400-122740400	Strong transcription	HSMM	muscle
49	chr4:122730400-122740600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr4:122730400-122742400	Strong transcription	HMEC	breast

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