Variant report

Variant	rs356142
Chromosome Location	chr9:97546145-97546146
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:31)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:31 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97390244..97393079-chr9:97544131..97546613,2	MCF-7	breast:
2	chr9:97537649..97550005-chr9:97763285..97775962,36	MCF-7	breast:
3	chr9:97544874..97546950-chr9:97556515..97558728,2	MCF-7	breast:
4	chr9:97545898..97547763-chr9:97631465..97634095,2	MCF-7	breast:
5	chr9:97543312..97547479-chr9:97579071..97582826,7	MCF-7	breast:
6	chr9:97545172..97548041-chr9:97865707..97867971,2	MCF-7	breast:
7	chr9:97545819..97548114-chr9:97554725..97556253,2	MCF-7	breast:
8	chr9:97543881..97546251-chr9:97877012..97878799,2	MCF-7	breast:
9	chr9:97543159..97549431-chr9:97764177..97768958,14	MCF-7	breast:
10	chr9:97543420..97548041-chr9:97751061..97760906,16	MCF-7	breast:
11	chr9:97544700..97548107-chr9:97891004..97896251,5	MCF-7	breast:
12	chr9:97544027..97547289-chr9:97566089..97570297,6	MCF-7	breast:
13	chr9:97544575..97547315-chr9:97798052..97799769,2	MCF-7	breast:
14	chr9:97544710..97547210-chr9:97761164..97763494,2	MCF-7	breast:
15	chr9:97544877..97546218-chr9:97753797..97756011,68	MCF-7	breast:
16	chr9:97544453..97547031-chr9:97714390..97716009,2	MCF-7	breast:
17	chr9:97542800..97546553-chr9:97773474..97777107,5	MCF-7	breast:
18	chr9:97544202..97547162-chr9:97884981..97887841,2	MCF-7	breast:
19	chr9:97544966..97548199-chr9:97548502..97553073,8	MCF-7	breast:
20	chr9:97544533..97546348-chr9:97748753..97750698,2	K562	blood:
21	chr9:97401002..97402082-chr9:97544824..97546198,12	MCF-7	breast:
22	chr9:97546073..97546668-chr9:117373481..117374080,2	MCF-7	breast:
23	chr9:97539932..97552626-chr9:97673836..97693079,64	MCF-7	breast:
24	chr9:97540504..97553156-chr9:97674790..97689428,56	MCF-7	breast:
25	chr9:97543978..97547772-chr9:97852128..97855870,5	MCF-7	breast:
26	chr9:97542228..97547641-chr9:97578377..97583453,10	MCF-7	breast:
27	chr9:97545480..97547938-chr9:97567296..97570948,4	MCF-7	breast:
28	chr9:97545780..97548611-chr9:97694354..97696585,2	MCF-7	breast:
29	chr9:97544221..97547787-chr9:97752281..97754950,4	MCF-7	breast:
30	chr9:97543390..97547292-chr9:97769751..97772749,5	MCF-7	breast:
31	chr9:97401002..97402082-chr9:97544824..97546198,18	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000157693	Chromatin interaction
ENSG00000148120	Chromatin interaction
ENSG00000165140	Chromatin interaction
ENSG00000223849	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10121865	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10122127	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10217427	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10732405	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10732406	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10733755	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10739986	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10761355	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10761359	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10821405	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10993348	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228614	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12339275	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12340251	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12344537	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12352276	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12553690	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12684703	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13285343	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16911661	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1810772	0.86[EUR][1000 genomes]
rs181488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187163	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs193292	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2119954	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2165715	0.85[AFR][1000 genomes]
rs2165716	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2304884	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2406899	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs242259	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2584803	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2584804	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2767403	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2767404	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28647286	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34940574	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356122	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356123	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356124	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356126	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356127	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356129	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs356130	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs356134	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356135	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356137	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356138	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356140	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356143	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356146	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs374708	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs376902	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380205	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs384039	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858087	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3858088	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs389365	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs396538	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs397617	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs400231	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs405110	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs415016	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs418764	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs439052	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4437717	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4537361	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs471161	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744377	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4744379	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744380	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744383	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4744388	0.85[AFR][1000 genomes]
rs55795862	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55914113	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55926255	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57504746	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58042095	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6479565	0.87[EUR][1000 genomes]
rs6479570	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479571	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479572	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479574	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6479577	0.83[AFR][1000 genomes]
rs672012	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67625382	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7025234	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7028317	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7030617	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7031172	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7031518	0.83[AMR][1000 genomes]
rs7041982	0.85[EUR][1000 genomes]
rs7045387	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7047864	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs732141	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7853126	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7861358	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7862700	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7869666	0.83[AMR][1000 genomes]
rs913182	0.87[EUR][1000 genomes]
rs9409806	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]

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
rs356142	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97523400-97552600	Weak transcription	Dnd41	blood
2	chr9:97523400-97554000	Weak transcription	Primary T cells from cord blood	blood
3	chr9:97523400-97557800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr9:97523400-97563800	Weak transcription	Fetal Kidney	kidney
5	chr9:97523600-97549400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:97523600-97552600	Weak transcription	Thymus	Thymus
7	chr9:97523600-97554400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr9:97524000-97553200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:97524200-97554600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr9:97524200-97554600	Weak transcription	Fetal Intestine Large	intestine
11	chr9:97526600-97549000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr9:97530200-97551200	Weak transcription	Primary B cells from cord blood	blood
13	chr9:97530200-97563000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:97531600-97563000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr9:97531600-97563000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:97533800-97555000	Weak transcription	GM12878-XiMat	blood
17	chr9:97535200-97547600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:97535800-97552600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:97536200-97557800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:97536400-97554600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:97541600-97547800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:97541600-97554800	Weak transcription	Right Ventricle	heart
23	chr9:97542400-97548600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr9:97543000-97553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:97543000-97553800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:97543200-97553000	Weak transcription	K562	blood
27	chr9:97544200-97546400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:97544400-97546600	Enhancers	NHDF-Ad	bronchial
29	chr9:97544600-97546200	Enhancers	A549	lung
30	chr9:97544600-97546400	Enhancers	Brain Angular Gyrus	brain
31	chr9:97544600-97546400	Enhancers	Brain Hippocampus Middle	brain
32	chr9:97544600-97546400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr9:97544600-97546400	Enhancers	HSMMtube	muscle
34	chr9:97544600-97546800	Enhancers	Hela-S3	cervix
35	chr9:97544600-97546800	Enhancers	HSMM	muscle
36	chr9:97545000-97546400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr9:97545000-97546400	Enhancers	HMEC	breast
38	chr9:97545000-97546600	Enhancers	Brain Substantia Nigra	brain
39	chr9:97545200-97546600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:97545400-97547000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:97545400-97552600	Weak transcription	Fetal Intestine Small	intestine
42	chr9:97545400-97556600	Weak transcription	Fetal Brain Male	brain
43	chr9:97545400-97567200	Weak transcription	Small Intestine	intestine
44	chr9:97545800-97546600	Enhancers	Osteobl	bone
45	chr9:97545800-97547400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:97545800-97547400	Weak transcription	HepG2	liver
47	chr9:97545800-97547600	Weak transcription	Brain Anterior Caudate	brain
48	chr9:97545800-97547600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr9:97545800-97547600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:97545800-97547800	Weak transcription	Stomach Mucosa	stomach

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