Variant report

Variant	rs10200949
Chromosome Location	chr2:98520222-98520223
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:98519901..98521401-chr2:98524345..98526039,2	K562	blood:
2	chr2:98519788..98522524-chr2:98522979..98525608,2	MCF-7	breast:
3	chr2:98505348..98508247-chr2:98519250..98521290,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10176201	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10182941	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10211231	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1071885	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865055	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11123924	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123949	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123966	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11690482	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11693874	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11888323	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11899171	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12712123	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12712174	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712176	0.83[ASN][1000 genomes]
rs13003978	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13006817	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13008503	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13010946	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13022778	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13034644	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1317178	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405546	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1466924	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503200	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1922280	1.00[ASN][1000 genomes]
rs1922282	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017028	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2091772	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2100058	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2141862	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279825	0.85[ASN][1000 genomes]
rs2279826	0.86[ASN][1000 genomes]
rs2309316	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309317	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2309356	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3088327	0.80[ASN][1000 genomes]
rs3762593	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4274643	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4560167	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5865	0.86[ASN][1000 genomes]
rs6543108	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6543109	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6543161	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543177	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543202	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6543210	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707924	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6709571	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6710813	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6719556	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6723466	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6723653	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6744331	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6748809	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6748927	0.91[ASN][1000 genomes]
rs7558931	0.81[EUR][1000 genomes]
rs7561104	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7562695	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7567397	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7574437	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7577886	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7582664	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586210	0.86[ASN][1000 genomes]
rs7598116	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7602412	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7605180	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs930607	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9308862	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956696	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973416	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10200949	TMEM131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98503600-98522800	Weak transcription	HUVEC	blood vessel
2	chr2:98503800-98522600	Weak transcription	Fetal Kidney	kidney
3	chr2:98503800-98522800	Weak transcription	K562	blood
4	chr2:98503800-98524800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:98503800-98528600	Weak transcription	NHDF-Ad	bronchial
6	chr2:98503800-98536400	Weak transcription	HSMMtube	muscle
7	chr2:98504000-98521800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:98504000-98521800	Weak transcription	Fetal Lung	lung
9	chr2:98504000-98522000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:98504000-98522200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:98504000-98522400	Weak transcription	Primary B cells from cord blood	blood
12	chr2:98504000-98522800	Weak transcription	Fetal Brain Female	brain
13	chr2:98504000-98523000	Weak transcription	Psoas Muscle	Psoas
14	chr2:98504000-98523600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:98504000-98528000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:98504000-98533800	Weak transcription	Spleen	Spleen
17	chr2:98504000-98538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:98504000-98540600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:98504000-98540800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:98504200-98522200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:98504200-98522200	Weak transcription	Fetal Stomach	stomach
22	chr2:98504200-98522200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:98504200-98522400	Weak transcription	Ovary	ovary
24	chr2:98504200-98522800	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:98504200-98523000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:98504200-98523000	Weak transcription	Left Ventricle	heart
27	chr2:98504200-98525400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:98504200-98530800	Weak transcription	Thymus	Thymus
29	chr2:98504400-98522000	Weak transcription	Placenta	Placenta
30	chr2:98504400-98522800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:98504400-98527000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:98504600-98521600	Weak transcription	Osteobl	bone
33	chr2:98504600-98522000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:98504600-98522200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:98504600-98522200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:98504600-98522400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:98504600-98522400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:98504600-98522400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:98504600-98522400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:98504600-98522800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:98504600-98523000	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:98504600-98523000	Weak transcription	Dnd41	blood
43	chr2:98504600-98523200	Weak transcription	Liver	Liver
44	chr2:98504600-98524200	Weak transcription	Adipose Nuclei	Adipose
45	chr2:98504600-98524200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:98504600-98525600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:98504600-98540800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:98504600-98552200	Weak transcription	NHLF	lung
49	chr2:98504800-98521400	Weak transcription	HepG2	liver
50	chr2:98504800-98521600	Weak transcription	Primary monocytes fromperipheralblood	blood

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