Variant report

Variant	rs16861235
Chromosome Location	chr3:113332969-113332970
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	POLR2A	chr3:113332861-113333059	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:113332798-113333428	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113331903..113333540-chr3:113337215..113339605,2	MCF-7	breast:
2	chr3:113327452..113329202-chr3:113332188..113334473,2	K562	blood:

Variant related genes	Relation type
SIDT1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10934239	0.81[AMR][1000 genomes]
rs10934240	0.81[AMR][1000 genomes]
rs11914863	0.86[AMR][1000 genomes]
rs11918910	0.86[AMR][1000 genomes]
rs11920913	0.81[AMR][1000 genomes]
rs11921407	0.86[AMR][1000 genomes]
rs12486414	0.93[AMR][1000 genomes]
rs12489192	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12490048	1.00[AMR][1000 genomes]
rs12490651	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12491540	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12492290	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12492542	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12492783	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12493602	0.93[AMR][1000 genomes]
rs12493935	0.81[AMR][1000 genomes]
rs12494777	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12495298	0.86[AMR][1000 genomes]
rs12495713	0.93[AMR][1000 genomes]
rs12496604	0.93[AMR][1000 genomes]
rs12496617	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12497754	0.93[AMR][1000 genomes]
rs16861230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16861233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16861331	0.93[AMR][1000 genomes]
rs2292512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2566972	0.81[AMR][1000 genomes]
rs2603791	0.81[AMR][1000 genomes]
rs3773686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57010522	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113285200-113343400	Weak transcription	Small Intestine	intestine
2	chr3:113320400-113333200	Weak transcription	Fetal Intestine Large	intestine
3	chr3:113320400-113345600	Weak transcription	Fetal Intestine Small	intestine
4	chr3:113320800-113347600	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr3:113321200-113333000	Weak transcription	Spleen	Spleen
6	chr3:113321200-113349200	Weak transcription	Brain Angular Gyrus	brain
7	chr3:113321200-113349600	Weak transcription	Lung	lung
8	chr3:113322600-113348600	Weak transcription	Colonic Mucosa	Colon
9	chr3:113323200-113342400	Weak transcription	Pancreas	Pancrea
10	chr3:113326000-113334000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:113326000-113334600	Weak transcription	Fetal Lung	lung
12	chr3:113326200-113335600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:113326200-113340000	Weak transcription	Fetal Stomach	stomach
14	chr3:113326200-113340600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr3:113326600-113335600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:113326600-113340600	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:113326600-113350000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:113326800-113335400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:113326800-113340400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:113326800-113344800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:113326800-113349200	Strong transcription	GM12878-XiMat	blood
22	chr3:113326800-113350200	Strong transcription	Primary T cells from cord blood	blood
23	chr3:113327200-113338400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr3:113327400-113339200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:113327400-113340400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:113327600-113338400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:113328400-113335200	Strong transcription	Fetal Thymus	thymus
28	chr3:113329000-113334400	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:113329200-113333000	Strong transcription	Primary B cells from cord blood	blood
30	chr3:113329400-113336400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:113329800-113334200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:113330000-113333000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:113330400-113333200	Weak transcription	Thymus	Thymus
34	chr3:113330400-113339000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:113331400-113345400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:113332000-113333000	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr3:113332000-113333800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:113332000-113335400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:113332200-113333000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:113332200-113333000	Weak transcription	Psoas Muscle	Psoas
41	chr3:113332200-113338000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:113332200-113342600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:113332400-113334200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr3:113332400-113338600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:113332400-113346600	Weak transcription	Gastric	stomach
46	chr3:113332400-113349200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:113332600-113333000	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr3:113332600-113334600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:113332600-113342200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:113332800-113333000	Enhancers	Adipose Nuclei	Adipose

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