Variant report

Variant	rs400231
Chromosome Location	chr9:97533176-97533177
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97520861..97523469-chr9:97531163..97533189,3	MCF-7	breast:
2	chr9:97529861..97533578-chr9:97534032..97536715,3	K562	blood:
3	chr9:97525840..97529015-chr9:97532404..97535563,3	K562	blood:
4	chr9:97530626..97534561-chr9:97683586..97686603,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10121865	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10122127	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10217427	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732405	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10732406	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10733755	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10739986	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10739991	0.85[YRI][hapmap]
rs10761355	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10761359	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10821405	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10993348	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10993351	0.86[YRI][hapmap]
rs1113967	0.82[YRI][hapmap]
rs1228614	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12339275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340251	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553690	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12684703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13285343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1530331	0.90[YRI][hapmap]
rs16911661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810772	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs181488	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs187163	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193292	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119953	0.82[YRI][hapmap]
rs2119954	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2165716	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2304884	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2406899	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs242259	0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2584803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2584804	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2767403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2767404	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28647286	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2897523	0.82[YRI][hapmap]
rs34940574	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356123	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356126	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356127	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs356129	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356135	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356137	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356138	0.88[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356142	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs356143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374708	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376902	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs380205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384039	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3858087	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3858088	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3886568	0.80[YRI][hapmap]
rs389365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs396538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397617	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405110	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs415016	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs418764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4437717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537361	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs471161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4744379	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4744380	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4744383	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55795862	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55914113	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55926255	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57504746	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58042095	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479565	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6479570	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6479571	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6479572	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6479574	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs672012	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67625382	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025234	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7026714	1.00[YRI][hapmap]
rs7028317	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030617	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031172	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7031518	0.86[AMR][1000 genomes]
rs7035166	1.00[YRI][hapmap]
rs7041982	0.87[EUR][1000 genomes]
rs7045387	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7047864	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs732141	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7853126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7861358	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7862700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7870679	0.88[YRI][hapmap]
rs894428	1.00[YRI][hapmap]
rs913182	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9409806	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1041922	chr9:97444976-97536753	Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs400231	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97506200-97533400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:97509200-97536000	Weak transcription	Pancreas	Pancrea
3	chr9:97512600-97540800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:97512600-97544600	Weak transcription	Psoas Muscle	Psoas
5	chr9:97519800-97544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:97521800-97541200	Weak transcription	Right Ventricle	heart
7	chr9:97522400-97540400	Weak transcription	Fetal Heart	heart
8	chr9:97522800-97534600	Weak transcription	Fetal Brain Male	brain
9	chr9:97522800-97534600	Weak transcription	NHLF	lung
10	chr9:97523000-97534600	Weak transcription	Ovary	ovary
11	chr9:97523200-97535000	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:97523400-97533400	Weak transcription	Brain Substantia Nigra	brain
13	chr9:97523400-97533600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:97523400-97534400	Weak transcription	Osteobl	bone
15	chr9:97523400-97534600	Weak transcription	Right Atrium	heart
16	chr9:97523400-97535600	Weak transcription	Aorta	Aorta
17	chr9:97523400-97535800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:97523400-97541400	Weak transcription	NHEK	skin
19	chr9:97523400-97544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:97523400-97544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:97523400-97545200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:97523400-97545200	Weak transcription	Liver	Liver
23	chr9:97523400-97545200	Weak transcription	Lung	lung
24	chr9:97523400-97545400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:97523400-97552600	Weak transcription	Dnd41	blood
26	chr9:97523400-97554000	Weak transcription	Primary T cells from cord blood	blood
27	chr9:97523400-97557800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr9:97523400-97563800	Weak transcription	Fetal Kidney	kidney
29	chr9:97523600-97533600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:97523600-97534600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:97523600-97534600	Weak transcription	HSMM	muscle
32	chr9:97523600-97534600	Weak transcription	HSMMtube	muscle
33	chr9:97523600-97535200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:97523600-97535200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr9:97523600-97535600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr9:97523600-97535800	Weak transcription	HepG2	liver
37	chr9:97523600-97536000	Weak transcription	Spleen	Spleen
38	chr9:97523600-97540400	Weak transcription	A549	lung
39	chr9:97523600-97545000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:97523600-97545200	Weak transcription	Left Ventricle	heart
41	chr9:97523600-97549400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:97523600-97552600	Weak transcription	Thymus	Thymus
43	chr9:97523600-97554400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr9:97523800-97544200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr9:97524000-97534000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:97524000-97534400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:97524000-97534600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr9:97524000-97534600	Weak transcription	Fetal Thymus	thymus
49	chr9:97524000-97535200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr9:97524000-97535400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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