Variant report

Variant	rs10821160
Chromosome Location	chr9:96326127-96326128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96212024..96217170-chr9:96326121..96330116,7	MCF-7	breast:
2	chr9:96322191..96324124-chr9:96324483..96327194,2	K562	blood:
3	chr9:96324507..96327332-chr9:96327489..96329838,2	K562	blood:
4	chr9:96239972..96242150-chr9:96326116..96327649,2	MCF-7	breast:
5	chr9:96324653..96326761-chr9:96337595..96340198,2	MCF-7	breast:
6	chr9:96319216..96322786-chr9:96325553..96328069,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197724	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000263875	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10114002	0.81[CEU][hapmap]
rs10116422	0.81[CEU][hapmap]
rs10117225	0.81[CEU][hapmap]
rs10117691	0.88[CEU][hapmap]
rs10123378	0.81[CEU][hapmap]
rs10156602	0.85[CEU][hapmap];0.80[TSI][hapmap]
rs10512223	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1055710	0.83[GIH][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes]
rs10739950	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10761227	0.83[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs10761228	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10761229	0.89[ASW][hapmap];0.84[CEU][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10761230	0.84[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10761231	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10761232	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10761233	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10761235	0.90[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10761238	0.96[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs10761240	0.81[CEU][hapmap]
rs10761243	0.81[CEU][hapmap]
rs10821128	1.00[ASW][hapmap];0.81[CEU][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs10821129	1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs10821130	0.81[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs10821132	1.00[YRI][hapmap]
rs10821134	0.84[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10821136	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10821137	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10821138	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10821139	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10821140	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10821141	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10821142	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10821143	0.92[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10821145	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10821146	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10821147	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10821148	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10821150	0.95[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10821151	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10821152	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10821153	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10821154	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10821157	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10821158	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10821159	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821168	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs10821181	0.81[CEU][hapmap]
rs10992746	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992748	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992749	0.89[ASW][hapmap];0.84[CEU][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992751	0.85[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992754	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992756	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10992757	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10992759	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10992768	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10992769	1.00[YRI][hapmap]
rs10992770	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10992772	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10992779	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10992780	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10992781	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10992790	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10992792	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs10992797	0.81[CEU][hapmap]
rs10992804	0.81[CEU][hapmap]
rs11790060	0.88[AMR][1000 genomes]
rs11790449	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11791374	0.89[ASW][hapmap];0.84[CEU][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12376738	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12377399	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12377707	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12379660	0.83[TSI][hapmap]
rs12380167	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13285064	0.92[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13294381	0.83[EUR][1000 genomes]
rs1412048	0.81[CEU][hapmap]
rs1412050	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1556416	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16909199	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2150749	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2183760	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2297376	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2398845	0.81[CEU][hapmap]
rs34866682	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34883241	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36016074	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3813387	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3813388	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4307405	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4568663	0.81[CEU][hapmap]
rs4743922	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743923	0.89[ASW][hapmap];0.96[MEX][hapmap]
rs4743924	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4743928	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4744240	0.86[AMR][1000 genomes]
rs4744242	0.84[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4744247	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744249	0.89[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744250	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4744253	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4744254	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864396	1.00[ASW][hapmap];0.96[MEX][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7869969	0.83[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs882851	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][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	nsv1041803	chr9:96299639-96342013	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10821160	HIATL1	cis	parietal	SCAN
rs10821160	FAM120AOS	cis	parietal	SCAN
rs10821160	FAM120A	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96278400-96327000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr9:96278400-96327200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr9:96278400-96328200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr9:96279000-96327400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr9:96284600-96327200	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr9:96284600-96328200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:96284800-96327200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:96285000-96327000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:96285000-96327000	Strong transcription	Dnd41	blood
10	chr9:96285200-96327800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:96285400-96327800	Strong transcription	Liver	Liver
12	chr9:96299200-96326800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:96299400-96327800	Strong transcription	Placenta	Placenta
14	chr9:96301200-96327200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:96302000-96328000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:96304400-96328200	Strong transcription	Adipose Nuclei	Adipose
17	chr9:96305200-96326800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr9:96305200-96327000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr9:96305400-96327000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:96305400-96327200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:96305400-96327600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:96307600-96329000	Weak transcription	Right Atrium	heart
23	chr9:96311400-96326600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr9:96311400-96327000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:96311400-96327000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:96311400-96327000	Strong transcription	Fetal Thymus	thymus
27	chr9:96311600-96326800	Strong transcription	Primary hematopoietic stem cells	blood
28	chr9:96311800-96327000	Strong transcription	Fetal Intestine Large	intestine
29	chr9:96312000-96326600	Strong transcription	HUVEC	blood vessel
30	chr9:96312200-96326800	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr9:96312200-96327800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:96312400-96328000	Strong transcription	Hela-S3	cervix
33	chr9:96312600-96327000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr9:96312600-96329000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr9:96312800-96327000	Strong transcription	Osteobl	bone
36	chr9:96312800-96328200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr9:96313000-96327200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr9:96314000-96326800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr9:96314000-96327000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr9:96315000-96326800	Strong transcription	Primary T cells from cord blood	blood
41	chr9:96315600-96326200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr9:96316400-96326800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:96316600-96326800	Strong transcription	Left Ventricle	heart
44	chr9:96316600-96327200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:96316800-96327000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:96317000-96326800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr9:96317000-96326800	Strong transcription	Right Ventricle	heart
48	chr9:96317000-96327800	Strong transcription	HSMM	muscle
49	chr9:96317200-96326800	Strong transcription	Fetal Muscle Leg	muscle
50	chr9:96317400-96326800	Strong transcription	Skeletal Muscle Female	skeletal muscle

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