Variant report

Variant	rs11119904
Chromosome Location	chr1:212466604-212466605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr1:212466324-212466677	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212464233..212466790-chr1:212482649..212484293,2	K562	blood:
2	chr1:212464978..212469431-chr1:212471345..212474474,8	K562	blood:
3	chr1:212243541..212244748-chr1:212466553..212467549,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230063	TF binding region
ENSG00000225338	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10019	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12023488	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12024665	0.81[ASN][1000 genomes]
rs12033246	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12035647	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12036130	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12410664	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1389371	0.83[EUR][1000 genomes]
rs17042034	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1774249	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1992643	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2252044	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2298114	0.90[ASN][1000 genomes]
rs2516331	0.83[EUR][1000 genomes]
rs2589474	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3099112	0.87[EUR][1000 genomes]
rs351373	0.83[EUR][1000 genomes]
rs351377	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs351378	0.83[EUR][1000 genomes]
rs351379	0.83[EUR][1000 genomes]
rs351380	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs351386	0.83[EUR][1000 genomes]
rs351393	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs351398	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351401	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs351407	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs351408	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs351417	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs351419	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3767861	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3767862	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3767863	0.88[EUR][1000 genomes]
rs4951582	0.82[EUR][1000 genomes]
rs4951588	0.81[ASN][1000 genomes]
rs4951589	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6659594	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7415843	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7519959	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7521853	0.82[EUR][1000 genomes]
rs7544225	0.83[EUR][1000 genomes]
rs792445	0.85[EUR][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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv1799093	chr1:212447167-212468974	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1800932	chr1:212447167-212468974	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv1839997	chr1:212447167-212468974	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	esv1839887	chr1:212457414-212478047	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11119904	TMEM206	cis	Esophagus Mucosa	GTEx
rs11119904	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs11119904	NENF	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212460200-212489200	Weak transcription	Spleen	Spleen
2	chr1:212461000-212469000	Enhancers	Brain Substantia Nigra	brain
3	chr1:212461000-212476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:212461200-212467200	Enhancers	HMEC	breast
5	chr1:212461600-212468800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:212461800-212470200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:212462000-212471200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr1:212462200-212467200	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr1:212462200-212468800	Enhancers	Brain Anterior Caudate	brain
10	chr1:212462200-212471000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:212462200-212471000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:212462400-212467200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:212462400-212469000	Enhancers	Brain Cingulate Gyrus	brain
14	chr1:212462600-212471000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr1:212462800-212470000	Enhancers	Liver	Liver
16	chr1:212463200-212467400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:212463400-212467200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:212463600-212467600	Enhancers	K562	blood
19	chr1:212463600-212468800	Weak transcription	Thymus	Thymus
20	chr1:212463800-212471000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr1:212463800-212471000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:212464200-212467000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:212464200-212467200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:212464200-212467400	Enhancers	Duodenum Mucosa	Duodenum
25	chr1:212464200-212471200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:212464200-212483000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:212464400-212467200	Flanking Active TSS	GM12878-XiMat	blood
28	chr1:212464600-212467000	Enhancers	Primary B cells from cord blood	blood
29	chr1:212464600-212473000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:212464800-212467400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:212464800-212468600	Weak transcription	Gastric	stomach
32	chr1:212464800-212480200	Weak transcription	Lung	lung
33	chr1:212464800-212483800	Weak transcription	Pancreas	Pancrea
34	chr1:212464800-212506400	Weak transcription	Esophagus	oesophagus
35	chr1:212465000-212467200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr1:212465000-212467400	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr1:212465000-212468200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:212465000-212468800	Weak transcription	Colonic Mucosa	Colon
39	chr1:212465000-212469600	Enhancers	Adipose Nuclei	Adipose
40	chr1:212465000-212470400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:212465000-212474800	Weak transcription	Osteobl	bone
42	chr1:212465000-212480200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:212465200-212468200	Weak transcription	Right Ventricle	heart
44	chr1:212465200-212468400	Weak transcription	Hela-S3	cervix
45	chr1:212465400-212466800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:212465400-212466800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:212465400-212466800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:212465400-212466800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:212465400-212466800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:212465400-212467000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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