Variant report

Variant	rs7869666
Chromosome Location	chr9:97597137-97597138
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97594651..97597412-chr9:97683309..97685774,2	MCF-7	breast:
2	chr9:97591789..97593682-chr9:97596295..97598175,2	K562	blood:
3	chr9:97584341..97586520-chr9:97595155..97598117,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10121865	0.82[AMR][1000 genomes]
rs10122127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10512234	1.00[JPT][hapmap]
rs10512236	1.00[JPT][hapmap]
rs10732405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10732406	0.82[AMR][1000 genomes]
rs10739986	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10761355	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs10821405	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10993329	1.00[JPT][hapmap]
rs10993340	0.90[JPT][hapmap]
rs10993348	0.87[AMR][1000 genomes]
rs10993351	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1228614	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs12336437	0.86[JPT][hapmap]
rs12337706	1.00[JPT][hapmap]
rs12337992	1.00[JPT][hapmap]
rs12339275	0.80[CEU][hapmap]
rs12341764	1.00[JPT][hapmap]
rs12341814	1.00[JPT][hapmap]
rs12343530	1.00[JPT][hapmap]
rs12344157	1.00[JPT][hapmap]
rs12347744	1.00[JPT][hapmap]
rs12348060	1.00[JPT][hapmap]
rs12352276	0.80[CEU][hapmap]
rs12352600	1.00[JPT][hapmap]
rs12684703	0.80[CEU][hapmap]
rs13285343	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs16911670	1.00[JPT][hapmap]
rs16911713	1.00[JPT][hapmap]
rs181488	0.83[AMR][1000 genomes]
rs187163	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs2119954	0.87[AMR][1000 genomes]
rs2165715	1.00[YRI][hapmap]
rs2165716	0.82[AMR][1000 genomes]
rs2304884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2406899	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs242259	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs2584803	0.80[AMR][1000 genomes]
rs2584804	0.87[AMR][1000 genomes]
rs2767403	0.82[AMR][1000 genomes]
rs2767404	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs356122	0.82[AMR][1000 genomes]
rs356123	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs356124	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs356126	0.82[AMR][1000 genomes]
rs356127	0.82[AMR][1000 genomes]
rs356129	0.82[AMR][1000 genomes]
rs356130	0.82[AMR][1000 genomes]
rs356134	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs356135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs356137	0.82[AMR][1000 genomes]
rs356138	0.82[AMR][1000 genomes]
rs356140	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs356142	0.83[AMR][1000 genomes]
rs356146	0.80[CEU][hapmap]
rs376902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs3808890	1.00[JPT][hapmap]
rs384039	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs3858087	0.82[AMR][1000 genomes]
rs3858088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs389365	0.80[CEU][hapmap]
rs405110	0.82[AMR][1000 genomes]
rs415016	0.85[AMR][1000 genomes]
rs418764	0.80[CEU][hapmap]
rs439052	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs4437717	0.80[CEU][hapmap]
rs4537361	0.82[AMR][1000 genomes]
rs4744377	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs4744379	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4744380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4744383	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55914113	0.80[AMR][1000 genomes]
rs55926255	0.82[AMR][1000 genomes]
rs6479570	0.87[AMR][1000 genomes]
rs6479571	0.87[AMR][1000 genomes]
rs6479572	0.87[AMR][1000 genomes]
rs6479574	1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7025100	0.91[YRI][hapmap]
rs7025234	0.82[AMR][1000 genomes]
rs7031172	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7045387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs732141	0.80[CEU][hapmap]
rs7861358	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs7862700	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs7866487	0.91[JPT][hapmap]
rs925813	1.00[JPT][hapmap]
rs9409806	0.82[AMR][1000 genomes]
rs9987803	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	esv1035383	chr9:97597133-97597137	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7869666	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97570000-97601400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr9:97571800-97622600	Weak transcription	Primary B cells from cord blood	blood
3	chr9:97572000-97601600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr9:97580600-97600200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:97581800-97609600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:97582000-97599400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:97585000-97609600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:97589200-97598800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:97589200-97600400	Weak transcription	Primary T cells from cord blood	blood
10	chr9:97589200-97602000	Weak transcription	Lung	lung
11	chr9:97589200-97605400	Weak transcription	Spleen	Spleen
12	chr9:97589200-97609400	Weak transcription	Pancreas	Pancrea
13	chr9:97589200-97622400	Weak transcription	Aorta	Aorta
14	chr9:97589400-97598600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:97590400-97598600	Weak transcription	Fetal Intestine Large	intestine
16	chr9:97590400-97602000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:97590600-97609600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:97590600-97616000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr9:97591000-97609200	Weak transcription	Osteobl	bone
20	chr9:97592200-97599800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:97592200-97608400	Weak transcription	HSMMtube	muscle
22	chr9:97592200-97609400	Weak transcription	NHDF-Ad	bronchial
23	chr9:97592600-97599200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr9:97594800-97597600	Weak transcription	A549	lung
25	chr9:97595000-97599600	Weak transcription	HSMM	muscle
26	chr9:97595800-97597200	Enhancers	Liver	Liver
27	chr9:97597000-97598400	Enhancers	HepG2	liver

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