Variant report

Variant	rs1507994
Chromosome Location	chr4:122749541-122749542
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	TCF12	chr4:122748827-122749572	SK-N-SH	brain:	n/a	n/a
2	JUN	chr4:122749001-122749747	K562	blood:	n/a	n/a
3	GATA1	chr4:122748861-122749555	K562	blood:	n/a	chr4:122749092-122749103
4	GATA3	chr4:122748949-122749583	SK-N-SH	brain:	n/a	n/a
5	JUND	chr4:122749010-122749613	K562	blood:	n/a	chr4:122749165-122749176
6	GATA3	chr4:122748829-122749620	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr4:122748840-122749595	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:122743548..122747768-chr4:122748127..122751699,7	K562	blood:
2	chr4:122743051..122746003-chr4:122747790..122749584,2	MCF-7	breast:

Variant related genes	Relation type
CCNA2	TF binding region
ENSG00000145386	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11098645	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11098646	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11098648	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11731570	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11731917	0.91[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12512876	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1396080	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1507995	0.83[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17452156	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2063165	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2071486	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]
rs2221628	0.91[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3217753	0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3217771	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3217773	0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3217780	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3828485	0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3924987	0.83[ASN][1000 genomes]
rs4077102	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4516739	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56077950	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56159666	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56311153	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58649165	0.83[EUR][1000 genomes]
rs61217486	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6534323	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67772833	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6815790	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6821305	1.00[ASN][1000 genomes]
rs6823818	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6826506	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6838153	0.83[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6855269	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72680779	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7660548	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7686084	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7686200	0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7691955	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs769238	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs769246	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7699776	0.91[CEU][hapmap];0.84[CHB][hapmap];0.97[EUR][1000 genomes];0.90[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
rs1507994	BBS7	cis	parietal	SCAN
rs1507994	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL
rs1507994	BBS7	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122745400-122750600	Weak transcription	Gastric	stomach
2	chr4:122745400-122750600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:122745400-122751200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:122745400-122753200	Weak transcription	Lung	lung
5	chr4:122745400-122767200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:122745400-122777600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:122745400-122790400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:122745400-122790600	Weak transcription	Small Intestine	intestine
9	chr4:122745600-122750400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:122745600-122750600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:122745600-122750600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:122745600-122750600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:122745600-122750600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:122745600-122750600	Weak transcription	Left Ventricle	heart
15	chr4:122745600-122750800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:122745600-122751800	Weak transcription	Ovary	ovary
17	chr4:122745600-122758000	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:122745600-122758600	Weak transcription	Fetal Kidney	kidney
19	chr4:122745600-122759800	Weak transcription	Fetal Thymus	thymus
20	chr4:122745600-122760400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:122745600-122762000	Weak transcription	Aorta	Aorta
22	chr4:122745600-122764000	Weak transcription	Colonic Mucosa	Colon
23	chr4:122745600-122766200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:122745600-122766600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:122745600-122767200	Weak transcription	Esophagus	oesophagus
26	chr4:122745600-122767200	Weak transcription	Right Ventricle	heart
27	chr4:122745600-122767800	Weak transcription	Pancreas	Pancrea
28	chr4:122745600-122767800	Weak transcription	Thymus	Thymus
29	chr4:122745600-122769200	Weak transcription	Hela-S3	cervix
30	chr4:122745600-122770000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr4:122745600-122781600	Weak transcription	Placenta	Placenta
32	chr4:122745600-122790400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:122745600-122790600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr4:122745600-122790800	Weak transcription	Psoas Muscle	Psoas
35	chr4:122745800-122750200	Weak transcription	Fetal Lung	lung
36	chr4:122745800-122750400	Weak transcription	Fetal Stomach	stomach
37	chr4:122745800-122750600	Weak transcription	Primary B cells from cord blood	blood
38	chr4:122745800-122750600	Weak transcription	Primary T cells from cord blood	blood
39	chr4:122745800-122750600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:122745800-122750600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:122745800-122750600	Weak transcription	NHEK	skin
42	chr4:122745800-122750800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:122745800-122750800	Weak transcription	Fetal Intestine Large	intestine
44	chr4:122745800-122750800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr4:122745800-122751200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:122745800-122752400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr4:122745800-122753000	Weak transcription	Brain Angular Gyrus	brain
48	chr4:122745800-122753200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr4:122745800-122753200	Weak transcription	Liver	Liver
50	chr4:122745800-122753800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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