Variant report

Variant	rs10173416
Chromosome Location	chr2:33464163-33464164
allele	A/C
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	POLR2A	chr2:33462226-33464749	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr2:33464036-33464230	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:33463966-33464314	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:33463263-33464568	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33463635..33465309-chr2:33474827..33476454,2	K562	blood:

Variant related genes	Relation type
LTBP1	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10048733	0.89[ASN][1000 genomes]
rs10084248	0.89[ASN][1000 genomes]
rs10167324	0.89[ASN][1000 genomes]
rs10167399	0.89[ASN][1000 genomes]
rs10170980	0.89[ASN][1000 genomes]
rs10189948	0.89[ASN][1000 genomes]
rs10195782	0.89[ASN][1000 genomes]
rs10201015	0.89[ASN][1000 genomes]
rs10201397	0.89[ASN][1000 genomes]
rs10201620	0.89[ASN][1000 genomes]
rs10204479	0.89[ASN][1000 genomes]
rs10205515	0.89[ASN][1000 genomes]
rs10514773	1.00[ASN][1000 genomes]
rs11675702	1.00[ASN][1000 genomes]
rs11686962	1.00[ASN][1000 genomes]
rs11691887	1.00[ASN][1000 genomes]
rs11692723	0.95[ASN][1000 genomes]
rs11886226	1.00[ASN][1000 genomes]
rs11886337	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11898777	0.89[ASN][1000 genomes]
rs13392128	0.84[ASN][1000 genomes]
rs13408945	0.89[ASN][1000 genomes]
rs13417478	0.84[ASN][1000 genomes]
rs13417974	0.84[ASN][1000 genomes]
rs13431080	0.84[ASN][1000 genomes]
rs17012612	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17012615	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17012621	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17012646	0.84[ASN][1000 genomes]
rs17012655	0.89[ASN][1000 genomes]
rs17012657	0.89[ASN][1000 genomes]
rs17012674	0.89[ASN][1000 genomes]
rs17012680	0.84[ASN][1000 genomes]
rs17012691	0.89[ASN][1000 genomes]
rs17012720	0.95[ASN][1000 genomes]
rs17012778	0.90[ASN][1000 genomes]
rs2004437	0.95[ASN][1000 genomes]
rs2290427	0.95[ASN][1000 genomes]
rs2290447	0.89[ASN][1000 genomes]
rs3769546	0.89[ASN][1000 genomes]
rs4578839	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4641915	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55852365	0.95[ASN][1000 genomes]
rs57095191	0.89[ASN][1000 genomes]
rs57119251	0.89[ASN][1000 genomes]
rs57408328	0.84[ASN][1000 genomes]
rs60523332	0.89[ASN][1000 genomes]
rs60912788	0.84[ASN][1000 genomes]
rs61609498	0.84[ASN][1000 genomes]
rs61754245	1.00[ASN][1000 genomes]
rs6543693	0.84[ASN][1000 genomes]
rs6543694	0.84[ASN][1000 genomes]
rs6543695	0.84[ASN][1000 genomes]
rs6543696	0.84[ASN][1000 genomes]
rs6543697	0.84[ASN][1000 genomes]
rs6706122	0.89[ASN][1000 genomes]
rs6718325	0.84[ASN][1000 genomes]
rs6722904	0.89[ASN][1000 genomes]
rs6728561	0.89[ASN][1000 genomes]
rs6730109	0.84[ASN][1000 genomes]
rs6730341	0.84[ASN][1000 genomes]
rs6734291	0.89[ASN][1000 genomes]
rs6746796	0.84[ASN][1000 genomes]
rs6752708	0.89[ASN][1000 genomes]
rs6757287	0.89[ASN][1000 genomes]
rs6757381	0.89[ASN][1000 genomes]
rs6760864	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72855723	0.84[ASN][1000 genomes]
rs72855746	0.89[ASN][1000 genomes]
rs72855774	0.89[ASN][1000 genomes]
rs72855787	0.89[ASN][1000 genomes]
rs72858037	0.89[ASN][1000 genomes]
rs72858071	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72858072	1.00[ASN][1000 genomes]
rs73927364	0.95[ASN][1000 genomes]
rs7583435	0.89[ASN][1000 genomes]
rs7603774	0.89[ASN][1000 genomes]
rs7606937	0.89[ASN][1000 genomes]
rs9308932	0.89[ASN][1000 genomes]
rs964701	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873790	chr2:33369582-33466483	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33403800-33489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:33442600-33467600	Weak transcription	Ovary	ovary
3	chr2:33442800-33471400	Weak transcription	Psoas Muscle	Psoas
4	chr2:33447400-33468200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:33449400-33466200	Weak transcription	Fetal Heart	heart
6	chr2:33449400-33475400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:33451800-33466200	Weak transcription	Left Ventricle	heart
8	chr2:33455800-33466800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:33455800-33470600	Weak transcription	Fetal Kidney	kidney
10	chr2:33461200-33464200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:33461200-33464200	Enhancers	HMEC	breast
12	chr2:33461200-33464200	Enhancers	Osteobl	bone
13	chr2:33461200-33465600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr2:33461200-33468600	Enhancers	HUVEC	blood vessel
15	chr2:33462000-33466200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:33462200-33465200	Weak transcription	HSMM	muscle
17	chr2:33462200-33467600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:33462600-33465200	Weak transcription	NHDF-Ad	bronchial
19	chr2:33462600-33467400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:33462800-33464400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:33463200-33465600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:33463400-33464200	Flanking Active TSS	A549	lung
23	chr2:33463400-33465200	Weak transcription	NH-A	brain
24	chr2:33463400-33466000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:33463600-33464400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:33463800-33464200	Enhancers	Colon Smooth Muscle	Colon
27	chr2:33463800-33465200	Weak transcription	NHLF	lung
28	chr2:33463800-33466200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:33463800-33468000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:33463800-33471400	Weak transcription	Aorta	Aorta
31	chr2:33464000-33468000	Weak transcription	NHEK	skin

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