Variant report

Variant	rs10512253
Chromosome Location	chr9:97828358-97828359
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97822176..97825096-chr9:97827855..97830416,5	MCF-7	breast:
2	chr9:97814331..97816887-chr9:97827066..97829674,2	MCF-7	breast:
3	chr9:97682234..97685097-chr9:97826323..97831388,4	MCF-7	breast:
4	chr9:97825460..97828452-chr9:97831131..97835733,4	MCF-7	breast:
5	chr9:97827183..97829097-chr9:97831797..97833372,2	K562	blood:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1004373	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10117370	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10119512	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10121760	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1020963	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10761364	0.82[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10761366	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10761368	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10761369	0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs10993427	0.89[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10993464	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10993467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1113102	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1412488	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1564234	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1571894	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1571895	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061800	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404295	0.87[JPT][hapmap]
rs2404302	0.91[CEU][hapmap];0.89[CHB][hapmap];0.94[YRI][hapmap]
rs2404305	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404456	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802454	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3802456	0.83[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3858089	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4537362	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743979	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743980	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743981	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4743982	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743984	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744422	0.83[CEU][hapmap];0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs4744423	0.83[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4744424	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744425	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744426	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744428	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4744430	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744431	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744435	0.92[CEU][hapmap];0.85[CHB][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4744436	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479588	0.83[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6479591	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479592	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7020709	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7021351	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7022452	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7043705	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7048786	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7048941	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7851173	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7854831	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7857679	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7862156	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7863291	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7865144	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7871218	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7873479	0.80[AMR][1000 genomes]
rs7873567	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs962229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10512253	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	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97818800-97830400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:97820000-97854200	Weak transcription	Fetal Brain Male	brain
4	chr9:97820400-97840800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:97820400-97843000	Weak transcription	Primary T cells from cord blood	blood
6	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr9:97821000-97838400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:97821200-97839000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:97821200-97839600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:97821400-97843200	Weak transcription	Fetal Brain Female	brain
11	chr9:97821800-97829600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr9:97821800-97835600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:97822000-97834600	Strong transcription	Hela-S3	cervix
14	chr9:97822200-97833200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:97822800-97830000	Enhancers	Psoas Muscle	Psoas
16	chr9:97822800-97830200	Genic enhancers	Left Ventricle	heart
17	chr9:97822800-97831600	Genic enhancers	Muscle Satellite Cultured Cells	--
18	chr9:97822800-97832800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
19	chr9:97822800-97845400	Weak transcription	Primary B cells from cord blood	blood
20	chr9:97823400-97830000	Genic enhancers	Pancreas	Pancrea
21	chr9:97823600-97834600	Strong transcription	NH-A	brain
22	chr9:97823600-97845000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr9:97824000-97828800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr9:97824200-97828400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:97824200-97832800	Strong transcription	Adipose Nuclei	Adipose
26	chr9:97824400-97828400	Genic enhancers	NHEK	skin
27	chr9:97824600-97829800	Genic enhancers	Right Ventricle	heart
28	chr9:97824600-97832200	Strong transcription	Fetal Lung	lung
29	chr9:97824800-97832000	Enhancers	Fetal Heart	heart
30	chr9:97824800-97844600	Weak transcription	Fetal Thymus	thymus
31	chr9:97825000-97829800	Genic enhancers	Fetal Intestine Small	intestine
32	chr9:97825000-97829800	Enhancers	Stomach Mucosa	stomach
33	chr9:97825200-97828400	Strong transcription	Placenta	Placenta
34	chr9:97825200-97841000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:97825400-97829000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:97825400-97830000	Genic enhancers	Colon Smooth Muscle	Colon
37	chr9:97825400-97830600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:97825400-97854400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr9:97825800-97828400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:97825800-97839200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr9:97825800-97843400	Weak transcription	Thymus	Thymus
42	chr9:97825800-97852600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:97826000-97842800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr9:97826200-97828400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:97826200-97829200	Enhancers	Brain Cingulate Gyrus	brain
46	chr9:97826200-97843200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr9:97826200-97847400	Weak transcription	HUVEC	blood vessel
48	chr9:97826400-97829200	Enhancers	Brain Hippocampus Middle	brain
49	chr9:97826400-97829800	Genic enhancers	HepG2	liver
50	chr9:97826400-97842800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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