Variant report

Variant	rs242259
Chromosome Location	chr9:97552788-97552789
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97550204..97553450-chr9:97554457..97557544,3	MCF-7	breast:
2	chr9:97544966..97548199-chr9:97548502..97553073,8	MCF-7	breast:
3	chr9:97540504..97553156-chr9:97674790..97689428,56	MCF-7	breast:
4	chr9:97551865..97553652-chr9:97754340..97757104,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10121865	0.90[CEU][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10122127	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10217427	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10512234	1.00[JPT][hapmap]
rs10512236	1.00[JPT][hapmap]
rs10732405	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10732406	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10733755	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10739986	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10761355	0.91[CEU][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10761359	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10821405	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10993329	1.00[JPT][hapmap]
rs10993340	0.91[JPT][hapmap]
rs10993348	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10993351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1228614	0.91[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12336437	0.86[JPT][hapmap]
rs12337706	1.00[JPT][hapmap]
rs12337992	1.00[JPT][hapmap]
rs12339275	0.91[CEU][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12340251	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12341764	1.00[JPT][hapmap]
rs12341814	1.00[JPT][hapmap]
rs12343530	1.00[JPT][hapmap]
rs12344157	1.00[JPT][hapmap]
rs12344537	0.90[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12347744	1.00[JPT][hapmap]
rs12348060	1.00[JPT][hapmap]
rs12352276	0.91[CEU][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12352600	1.00[JPT][hapmap]
rs12553690	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12684703	0.91[CEU][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13285343	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1530331	1.00[YRI][hapmap]
rs16911661	0.90[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16911670	1.00[JPT][hapmap]
rs16911713	1.00[JPT][hapmap]
rs1810772	0.86[EUR][1000 genomes]
rs181488	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187163	0.91[CEU][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs193292	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2119954	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2165716	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2304884	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2406898	0.83[YRI][hapmap]
rs2406899	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2584803	0.90[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2584804	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2767403	0.90[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2767404	0.91[CEU][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28647286	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34940574	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356122	0.90[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356123	0.91[CEU][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356124	0.91[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356126	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356127	0.90[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356129	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs356130	0.90[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356134	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356135	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356137	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356138	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356140	0.91[CEU][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356142	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356143	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356146	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs374708	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs376902	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380205	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3808890	1.00[JPT][hapmap]
rs384039	0.90[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858087	0.88[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3858088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs389365	0.91[CEU][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs396538	0.90[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs397617	0.90[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs400231	0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs405110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs415016	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs418764	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs439052	0.91[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4437717	0.91[CEU][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4537361	0.90[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs471161	0.90[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744377	0.91[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4744379	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744380	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744383	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55795862	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55914113	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55926255	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57504746	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58042095	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6479565	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479570	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479571	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479572	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479574	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6479576	0.88[YRI][hapmap]
rs672012	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67625382	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7025234	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7025934	0.90[YRI][hapmap]
rs7026714	0.87[YRI][hapmap]
rs7028317	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7030617	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7031172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7031518	0.87[AMR][1000 genomes]
rs7035166	0.90[YRI][hapmap]
rs7037652	0.84[AFR][1000 genomes]
rs7038519	0.87[YRI][hapmap]
rs7041982	0.85[EUR][1000 genomes]
rs7045387	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7047864	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs732141	0.91[CEU][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7853126	0.90[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7861358	0.91[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7862700	0.91[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7866487	0.92[JPT][hapmap]
rs7869666	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7870679	1.00[YRI][hapmap]
rs894428	0.88[YRI][hapmap]
rs913182	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs925813	1.00[JPT][hapmap]
rs9409806	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9987803	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs242259	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97523400-97554000	Weak transcription	Primary T cells from cord blood	blood
2	chr9:97523400-97557800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:97523400-97563800	Weak transcription	Fetal Kidney	kidney
4	chr9:97523600-97554400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr9:97524000-97553200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:97524200-97554600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr9:97524200-97554600	Weak transcription	Fetal Intestine Large	intestine
8	chr9:97530200-97563000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:97531600-97563000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:97531600-97563000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:97533800-97555000	Weak transcription	GM12878-XiMat	blood
12	chr9:97536200-97557800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:97536400-97554600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr9:97541600-97554800	Weak transcription	Right Ventricle	heart
15	chr9:97543000-97553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:97543000-97553800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:97543200-97553000	Weak transcription	K562	blood
18	chr9:97545400-97556600	Weak transcription	Fetal Brain Male	brain
19	chr9:97545400-97567200	Weak transcription	Small Intestine	intestine
20	chr9:97545800-97553200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr9:97545800-97553800	Weak transcription	Fetal Stomach	stomach
22	chr9:97545800-97554400	Weak transcription	Brain Germinal Matrix	brain
23	chr9:97545800-97554400	Weak transcription	Fetal Lung	lung
24	chr9:97545800-97554400	Weak transcription	Left Ventricle	heart
25	chr9:97545800-97554400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:97545800-97554600	Weak transcription	Aorta	Aorta
27	chr9:97545800-97554600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:97545800-97554600	Weak transcription	Placenta	Placenta
29	chr9:97545800-97554600	Weak transcription	Lung	lung
30	chr9:97545800-97554600	Weak transcription	NHLF	lung
31	chr9:97545800-97556000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:97545800-97556400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:97545800-97560600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:97545800-97562200	Weak transcription	Ovary	ovary
35	chr9:97545800-97562200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr9:97545800-97563000	Weak transcription	Adipose Nuclei	Adipose
37	chr9:97545800-97563000	Weak transcription	Gastric	stomach
38	chr9:97545800-97563000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr9:97545800-97563000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr9:97545800-97563200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:97545800-97567000	Weak transcription	Fetal Brain Female	brain
42	chr9:97546000-97553600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:97546000-97554400	Weak transcription	Liver	Liver
44	chr9:97546000-97554400	Weak transcription	NH-A	brain
45	chr9:97546000-97554600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:97546000-97554800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr9:97546000-97560400	Weak transcription	Pancreas	Pancrea
48	chr9:97546000-97561400	Weak transcription	Colon Smooth Muscle	Colon
49	chr9:97546000-97562400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr9:97546600-97554200	Weak transcription	Osteobl	bone

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