Variant report

Variant	rs8041090
Chromosome Location	chr15:99646907-99646908
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	TCF7L2	chr15:99646425-99647028	Hela-S3	cervix:	n/a	n/a
2	SMC3	chr15:99644884-99647125	SK-N-SH	brain:	n/a	chr15:99645149-99645159
3	POLR2A	chr15:99644995-99647972	IMR90	lung:	n/a	n/a
4	TCF7L2	chr15:99645056-99647218	PANC-1	pancreas:	n/a	n/a
5	RCOR1	chr15:99644802-99647324	IMR90	lung:	n/a	n/a
6	RCOR1	chr15:99646855-99646996	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000259475	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10444900	0.82[EUR][1000 genomes]
rs10444901	0.82[EUR][1000 genomes]
rs13853	0.80[EUR][1000 genomes]
rs1466191	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1670238	0.82[EUR][1000 genomes]
rs1670247	0.87[ASN][1000 genomes]
rs1703775	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1703781	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1703783	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs260086	0.80[EUR][1000 genomes]
rs28617660	0.82[EUR][1000 genomes]
rs28690249	0.82[EUR][1000 genomes]
rs5030691	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62023639	0.80[ASN][1000 genomes]
rs62023640	0.83[EUR][1000 genomes]
rs62023641	0.83[EUR][1000 genomes]
rs62023642	0.83[EUR][1000 genomes]
rs62025370	0.90[ASN][1000 genomes]
rs62025375	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7170268	0.80[EUR][1000 genomes]
rs7176156	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7176176	0.80[EUR][1000 genomes]
rs8031137	0.83[EUR][1000 genomes]
rs8038315	0.82[EUR][1000 genomes]
rs8043501	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv904544	chr15:99524865-99655744	Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
15	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer 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 target site	30 gene(s)	inside rSNPs	diseases
16	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking 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 target site	31 gene(s)	inside rSNPs	diseases
17	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
19	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
20	esv3364884	chr15:99643929-99647227	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99644800-99647200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:99645000-99647000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:99645000-99647000	Active TSS	Brain Cingulate Gyrus	brain
4	chr15:99645000-99647400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:99645000-99647600	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr15:99645000-99648000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
7	chr15:99645000-99648200	Active TSS	Right Atrium	heart
8	chr15:99645000-99649600	Active TSS	Rectal Smooth Muscle	rectum
9	chr15:99645200-99647000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr15:99645200-99647200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:99645200-99647200	Active TSS	GM12878-XiMat	blood
12	chr15:99645200-99647400	Active TSS	Aorta	Aorta
13	chr15:99645200-99647400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
14	chr15:99645200-99647400	Active TSS	Left Ventricle	heart
15	chr15:99645200-99648200	Active TSS	Psoas Muscle	Psoas
16	chr15:99645200-99648400	Active TSS	Colon Smooth Muscle	Colon
17	chr15:99645400-99647200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:99646000-99648000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr15:99646000-99648000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
20	chr15:99646200-99647000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr15:99646200-99647000	Bivalent Enhancer	Stomach Mucosa	stomach
22	chr15:99646200-99647400	Bivalent Enhancer	Fetal Lung	lung
23	chr15:99646200-99647400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
24	chr15:99646200-99647600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
25	chr15:99646200-99648000	Enhancers	HepG2	liver
26	chr15:99646200-99648200	Flanking Active TSS	Hela-S3	cervix
27	chr15:99646400-99647000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:99646400-99647000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
29	chr15:99646400-99647200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:99646400-99647200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
31	chr15:99646400-99647400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr15:99646400-99647400	Bivalent/Poised TSS	Colonic Mucosa	Colon
33	chr15:99646400-99647400	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr15:99646400-99648200	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr15:99646400-99663200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:99646600-99647000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
37	chr15:99646600-99647000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:99646600-99647000	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr15:99646600-99647000	Bivalent Enhancer	Fetal Brain Female	brain
40	chr15:99646600-99647000	Active TSS	Pancreas	Pancrea
41	chr15:99646600-99647200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
42	chr15:99646600-99647400	Active TSS	Lung	lung
43	chr15:99646600-99647600	Active TSS	Esophagus	oesophagus
44	chr15:99646600-99647600	Weak transcription	HMEC	breast
45	chr15:99646600-99647800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
46	chr15:99646600-99647800	Flanking Active TSS	A549	lung
47	chr15:99646600-99648000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:99646600-99648000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
49	chr15:99646600-99648000	Enhancers	Liver	Liver
50	chr15:99646600-99648000	Active TSS	Right Ventricle	heart

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