Variant report

Variant	rs10199199
Chromosome Location	chr2:99061834-99061835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99059903..99063646-chr2:99224086..99226361,3	MCF-7	breast:
2	chr2:99061518..99063442-chr2:99098258..99101170,2	MCF-7	breast:
3	chr2:99060131..99062941-chr2:99132482..99135840,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000040933	Chromatin interaction
ENSG00000183513	Chromatin interaction
ENSG00000115446	Chromatin interaction

Extended variants
information (count: 163 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs10496327	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10514774	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1139829	0.82[EUR][1000 genomes]
rs11537554	0.81[EUR][1000 genomes]
rs11884553	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11888595	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11896729	0.83[EUR][1000 genomes]
rs11901568	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11902825	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12052639	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12617721	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12618524	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12619665	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12622341	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13402379	0.82[EUR][1000 genomes]
rs1516085	0.81[EUR][1000 genomes]
rs1587835	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17031139	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17031146	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17031905	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17032120	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17032866	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17032870	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17033136	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17033813	0.80[EUR][1000 genomes]
rs17034171	0.83[EUR][1000 genomes]
rs17034241	0.83[EUR][1000 genomes]
rs17444095	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17446058	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17502889	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17504774	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17505088	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17505326	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17506535	0.82[EUR][1000 genomes]
rs17513468	0.81[EUR][1000 genomes]
rs1847550	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230388	0.81[EUR][1000 genomes]
rs2276603	0.82[EUR][1000 genomes]
rs2278206	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2278207	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278208	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278211	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2278212	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2278213	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2278214	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2309390	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3203856	0.82[EUR][1000 genomes]
rs34906456	0.82[EUR][1000 genomes]
rs3729568	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3754871	0.83[EUR][1000 genomes]
rs3754872	0.83[EUR][1000 genomes]
rs3754875	0.81[EUR][1000 genomes]
rs3754877	0.81[EUR][1000 genomes]
rs3754878	0.84[EUR][1000 genomes]
rs3754879	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3754880	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3754881	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3754883	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3754884	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3754885	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3754886	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3754888	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3754889	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3754890	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3754891	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3754892	0.86[ASN][1000 genomes]
rs3754893	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769698	0.81[EUR][1000 genomes]
rs3769701	0.82[EUR][1000 genomes]
rs3769708	0.81[EUR][1000 genomes]
rs3769709	0.81[EUR][1000 genomes]
rs3769712	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3769713	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769715	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769716	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769717	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769719	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769723	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769724	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769725	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769726	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769727	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769728	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769729	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769730	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3769733	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3769734	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769735	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3769736	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769737	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769738	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3769740	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769741	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769743	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820941	0.81[EUR][1000 genomes]
rs3820943	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3820945	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4596026	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4599165	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4850874	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4850875	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4850876	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4850877	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4850878	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4850879	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4851131	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4851136	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4851140	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851141	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851142	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851144	0.82[EUR][1000 genomes]
rs4851145	0.83[EUR][1000 genomes]
rs4851146	0.81[EUR][1000 genomes]
rs55900716	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55934321	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56091613	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56118505	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56141907	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56197140	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56232707	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56240302	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56333112	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56357378	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58778964	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61180742	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6542754	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6728891	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6736755	0.83[EUR][1000 genomes]
rs6753380	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6753515	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72819965	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72819970	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72819971	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72819972	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72819981	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72819996	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72820002	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72821904	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72821907	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72821908	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72821920	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72821924	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72821930	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72821939	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72821943	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72821946	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72821951	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72821955	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72821956	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72821965	0.82[EUR][1000 genomes]
rs72823788	0.82[EUR][1000 genomes]
rs72823792	0.83[EUR][1000 genomes]
rs72823794	0.83[EUR][1000 genomes]
rs72823796	0.83[EUR][1000 genomes]
rs7562232	0.83[EUR][1000 genomes]
rs7585747	0.83[EUR][1000 genomes]
rs7585939	0.83[EUR][1000 genomes]
rs7588254	0.83[EUR][1000 genomes]
rs7593615	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595120	0.81[EUR][1000 genomes]
rs961242	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1006328	chr2:98977192-99210376	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10199199	UNC50	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99060600-99062000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr2:99060600-99062000	Active TSS	Duodenum Mucosa	Duodenum
3	chr2:99060600-99062000	Active TSS	Placenta Amnion	Placenta Amnion
4	chr2:99060600-99062000	Active TSS	Stomach Smooth Muscle	stomach
5	chr2:99060600-99062000	Active TSS	HSMMtube	muscle
6	chr2:99060600-99062200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:99060600-99062200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:99060600-99062400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr2:99060600-99062400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:99060600-99062400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:99060600-99062400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:99060600-99062400	Active TSS	A549	lung
13	chr2:99060600-99062400	Active TSS	GM12878-XiMat	blood
14	chr2:99060600-99062600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr2:99060800-99062000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:99060800-99062000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:99060800-99062000	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr2:99060800-99062000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:99060800-99062000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr2:99060800-99062000	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr2:99060800-99062000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:99060800-99062000	Active TSS	Brain Angular Gyrus	brain
23	chr2:99060800-99062000	Active TSS	Brain Hippocampus Middle	brain
24	chr2:99060800-99062000	Active TSS	Fetal Muscle Leg	muscle
25	chr2:99060800-99062000	Active TSS	Fetal Stomach	stomach
26	chr2:99060800-99062000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr2:99060800-99062000	Active TSS	Hela-S3	cervix
28	chr2:99060800-99062200	Active TSS	H9 Cell Line	embryonic stem cell
29	chr2:99060800-99062200	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr2:99060800-99062200	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr2:99060800-99062200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:99060800-99062200	Active TSS	Brain Cingulate Gyrus	brain
33	chr2:99060800-99062200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:99060800-99062200	Active TSS	Brain Substantia Nigra	brain
35	chr2:99060800-99062200	Active TSS	Colonic Mucosa	Colon
36	chr2:99060800-99062200	Active TSS	Colon Smooth Muscle	Colon
37	chr2:99060800-99062200	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr2:99060800-99062200	Active TSS	Left Ventricle	heart
39	chr2:99060800-99062200	Active TSS	Ovary	ovary
40	chr2:99060800-99062200	Active TSS	Pancreas	Pancrea
41	chr2:99060800-99062200	Active TSS	Psoas Muscle	Psoas
42	chr2:99060800-99062200	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr2:99060800-99062200	Active TSS	Right Atrium	heart
44	chr2:99060800-99062200	Active TSS	Right Ventricle	heart
45	chr2:99060800-99062200	Active TSS	Small Intestine	intestine
46	chr2:99060800-99062200	Active TSS	HMEC	breast
47	chr2:99060800-99062200	Active TSS	HSMM	muscle
48	chr2:99060800-99062200	Active TSS	NHLF	lung
49	chr2:99060800-99062400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:99060800-99062400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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