Variant report

Variant	rs2250673
Chromosome Location	chr11:57268170-57268171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57267671-57270190	K562	blood:	n/a	n/a
2	POLR2A	chr11:57267891-57269087	HL-60	blood:	n/a	n/a
3	POLR2A	chr11:57266861-57268576	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57260621..57264536-chr11:57264640..57268839,7	K562	blood:
2	chr11:57227341..57230250-chr11:57267205..57269644,2	K562	blood:
3	chr11:57194058..57195845-chr11:57267357..57269723,2	K562	blood:
4	chr11:57264825..57270955-chr11:57280277..57284813,10	K562	blood:
5	chr11:57265680..57269520-chr11:57278275..57283954,6	K562	blood:

No data

Variant related genes	Relation type
SLC43A1	TF binding region
ENSG00000149150	Chromatin interaction
ENSG00000186907	Chromatin interaction
ENSG00000134802	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1001956	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10750864	0.81[AMR][1000 genomes]
rs2258835	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2467327	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2509899	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511984	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511986	0.91[ASN][1000 genomes]
rs2581921	0.83[ASN][1000 genomes]
rs2581922	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581923	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2584856	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2584862	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2649667	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729353	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2729363	0.80[ASN][1000 genomes]
rs2729377	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2729384	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729387	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729394	0.82[ASN][1000 genomes]
rs2848626	0.90[ASN][1000 genomes]
rs2848634	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2848635	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2848640	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2250673	TIMM10	cis	multi-tissue	Pritchard
rs2250673	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2250673	TIMM10	cis	Esophagus Muscularis	GTEx
rs2250673	TIMM10	cis	Thyroid	GTEx
rs2250673	TIMM10	cis	Skin Sun Exposed Lower leg	GTEx
rs2250673	TIMM10	cis	Artery Tibial	GTEx
rs2250673	TIMM10	cis	Artery Aorta	GTEx
rs2250673	TIMM10	cis	Heart Left Ventricle	GTEx
rs2250673	TIMM10	cis	Muscle Skeletal	GTEx
rs2250673	TIMM10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57251200-57280600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr11:57251400-57279200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr11:57251400-57281200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr11:57253800-57276400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:57253800-57279000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:57255200-57269600	Weak transcription	Esophagus	oesophagus
7	chr11:57256400-57273000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:57257400-57281400	Weak transcription	Primary T cells from cord blood	blood
9	chr11:57258800-57279200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:57259200-57279000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr11:57259200-57280800	Weak transcription	GM12878-XiMat	blood
12	chr11:57261400-57281400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:57261800-57279600	Weak transcription	Dnd41	blood
14	chr11:57263000-57270000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:57264800-57269800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:57266000-57270000	Enhancers	Right Atrium	heart
17	chr11:57266800-57268200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:57266800-57268200	Enhancers	Fetal Thymus	thymus
19	chr11:57266800-57268200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr11:57266800-57268200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr11:57266800-57268400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:57266800-57269000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:57266800-57269000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr11:57266800-57269000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:57267200-57268800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr11:57267200-57279400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr11:57267400-57268200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr11:57267400-57268800	Genic enhancers	Spleen	Spleen
29	chr11:57267600-57268200	Genic enhancers	Fetal Intestine Small	intestine
30	chr11:57267600-57268200	Enhancers	Fetal Muscle Trunk	muscle
31	chr11:57267600-57268200	Enhancers	Fetal Muscle Leg	muscle
32	chr11:57267600-57269000	Enhancers	Left Ventricle	heart
33	chr11:57267600-57269000	Genic enhancers	Pancreas	Pancrea
34	chr11:57267600-57269200	Enhancers	Right Ventricle	heart
35	chr11:57267600-57270000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr11:57267600-57270000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr11:57267600-57270800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr11:57267600-57274600	Genic enhancers	HepG2	liver
39	chr11:57267600-57280200	Weak transcription	Primary B cells from cord blood	blood
40	chr11:57267600-57281200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr11:57267600-57281600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:57267800-57268200	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr11:57267800-57268200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:57267800-57268200	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr11:57267800-57268200	Enhancers	Adipose Nuclei	Adipose
46	chr11:57267800-57268200	Enhancers	Brain Angular Gyrus	brain
47	chr11:57267800-57268200	Enhancers	Brain Anterior Caudate	brain
48	chr11:57267800-57268200	Enhancers	Colon Smooth Muscle	Colon
49	chr11:57267800-57268200	Enhancers	Fetal Brain Female	brain
50	chr11:57267800-57268200	Enhancers	Fetal Kidney	kidney

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