Variant report

Variant	rs28508235
Chromosome Location	chr15:44603210-44603211
allele	A/G
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	NFIC	chr15:44603198-44603862	GM12878	blood:	n/a	n/a
2	RUNX3	chr15:44603209-44603871	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000203573	TF binding region
ENSG00000203574	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10152710	0.88[EUR][1000 genomes]
rs1021800	0.88[EUR][1000 genomes]
rs10467977	0.94[EUR][1000 genomes]
rs12591178	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12591581	0.88[EUR][1000 genomes]
rs12591811	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592995	0.94[EUR][1000 genomes]
rs12593125	0.94[EUR][1000 genomes]
rs12593325	0.88[EUR][1000 genomes]
rs12593686	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12593943	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594110	0.88[EUR][1000 genomes]
rs12594139	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594167	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12594621	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594645	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594746	0.94[EUR][1000 genomes]
rs12595484	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17551416	0.88[EUR][1000 genomes]
rs2055061	0.94[EUR][1000 genomes]
rs2288341	0.88[EUR][1000 genomes]
rs2288342	0.94[EUR][1000 genomes]
rs2303577	0.88[EUR][1000 genomes]
rs2303578	0.82[EUR][1000 genomes]
rs2412883	0.94[EUR][1000 genomes]
rs2412909	0.94[EUR][1000 genomes]
rs2433350	0.94[EUR][1000 genomes]
rs2555353	0.94[EUR][1000 genomes]
rs2556566	0.94[EUR][1000 genomes]
rs2556567	0.88[EUR][1000 genomes]
rs28561508	0.94[EUR][1000 genomes]
rs2899113	0.88[EUR][1000 genomes]
rs35555389	0.94[EUR][1000 genomes]
rs3784565	0.94[EUR][1000 genomes]
rs3784567	0.94[EUR][1000 genomes]
rs3809471	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3816928	0.94[EUR][1000 genomes]
rs3986142	0.94[EUR][1000 genomes]
rs3986143	0.94[EUR][1000 genomes]
rs4415978	0.94[EUR][1000 genomes]
rs4477677	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4577056	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924746	1.00[ASN][1000 genomes]
rs57270586	0.94[EUR][1000 genomes]
rs58956090	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59230801	0.94[EUR][1000 genomes]
rs59997416	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60003667	0.94[EUR][1000 genomes]
rs60399672	0.94[EUR][1000 genomes]
rs61185650	0.94[EUR][1000 genomes]
rs61234123	0.94[EUR][1000 genomes]
rs61258861	0.94[EUR][1000 genomes]
rs61278540	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61329003	0.94[EUR][1000 genomes]
rs61501839	0.94[EUR][1000 genomes]
rs6493103	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7162671	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7162802	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7163529	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7164709	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7166278	0.94[EUR][1000 genomes]
rs7166945	0.94[EUR][1000 genomes]
rs7167752	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7169333	0.94[EUR][1000 genomes]
rs7170248	0.94[EUR][1000 genomes]
rs7172106	0.94[EUR][1000 genomes]
rs7175200	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7178318	0.94[EUR][1000 genomes]
rs7179894	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7181772	0.94[EUR][1000 genomes]
rs7183109	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8023453	0.94[EUR][1000 genomes]
rs8024623	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8024805	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8025727	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8025876	0.94[EUR][1000 genomes]
rs8025955	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8026945	0.94[EUR][1000 genomes]
rs8027036	0.94[EUR][1000 genomes]
rs8028509	0.94[EUR][1000 genomes]
rs8028907	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8032079	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037395	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs883943	0.94[EUR][1000 genomes]
rs9672237	0.94[EUR][1000 genomes]
rs9673085	0.94[EUR][1000 genomes]
rs9806725	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[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	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
2	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
3	nsv1052511	chr15:44266441-44719023	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv542371	chr15:44266441-44719023	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats 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	29 gene(s)	inside rSNPs	diseases
5	esv3410956	chr15:44425145-44823647	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1044686	chr15:44489534-44697482	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv1043822	chr15:44491220-44686957	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv1035386	chr15:44498905-44677174	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv904177	chr15:44582886-44821843	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv569299	chr15:44598642-44776075	Weak transcription Flanking Active TSS Enhancers Strong 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	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44582000-44639400	Weak transcription	Lung	lung
2	chr15:44582800-44672200	Weak transcription	HSMM	muscle
3	chr15:44583000-44639400	Weak transcription	Fetal Lung	lung
4	chr15:44583200-44639200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr15:44583800-44639200	Weak transcription	Brain Germinal Matrix	brain
6	chr15:44584200-44625600	Weak transcription	Fetal Brain Female	brain
7	chr15:44585400-44628200	Weak transcription	Thymus	Thymus
8	chr15:44589000-44619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:44589000-44631600	Weak transcription	Left Ventricle	heart
10	chr15:44589200-44626400	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:44589400-44607000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:44589400-44607600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:44589600-44605600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:44589600-44617400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:44589800-44625200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:44589800-44632000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:44589800-44632400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr15:44589800-44632400	Weak transcription	NHLF	lung
19	chr15:44591400-44632800	Weak transcription	Hela-S3	cervix
20	chr15:44592800-44617600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:44592800-44639800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr15:44593000-44605800	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:44593200-44621200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:44593200-44625600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:44593200-44639200	Weak transcription	K562	blood
26	chr15:44593200-44639400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:44593600-44621200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:44593800-44607000	Weak transcription	Fetal Intestine Large	intestine
29	chr15:44593800-44607800	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:44593800-44613200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:44593800-44639400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:44595200-44631600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr15:44597200-44610800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:44597800-44613200	Weak transcription	Fetal Stomach	stomach
35	chr15:44597800-44623200	Weak transcription	Fetal Intestine Small	intestine
36	chr15:44598400-44607000	Weak transcription	Brain Substantia Nigra	brain
37	chr15:44598400-44628600	Weak transcription	Primary T cells from cord blood	blood
38	chr15:44598600-44646800	Weak transcription	Right Ventricle	heart
39	chr15:44599000-44606800	Weak transcription	Brain Anterior Caudate	brain
40	chr15:44599400-44605400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:44599600-44632600	Weak transcription	HSMMtube	muscle
42	chr15:44600800-44632400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:44601000-44620800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr15:44601000-44624800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:44601200-44621200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:44601400-44604200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:44601600-44617400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:44601600-44638600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:44602000-44607000	Weak transcription	A549	lung
50	chr15:44602200-44614000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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