Variant report

Variant	rs17022034
Chromosome Location	chr2:99486848-99486849
allele	A/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	ELF1	chr2:99485380-99486856	MCF-7	breast:	n/a	chr2:99485849-99485862 chr2:99485850-99485861 chr2:99485851-99485860
2	MAX	chr2:99485624-99486876	MCF-7	breast:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
3	RFX5	chr2:99485476-99486905	Hela-S3	cervix:	n/a	chr2:99486633-99486641
4	RFX5	chr2:99486226-99487287	SK-N-SH	brain:	n/a	chr2:99487133-99487142 chr2:99486633-99486641
5	HDAC2	chr2:99485396-99486857	MCF-7	breast:	n/a	n/a
6	MAX	chr2:99485535-99486886	ECC-1	luminal epithelium:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
7	NFIC	chr2:99485582-99486976	ECC-1	luminal epithelium:	n/a	chr2:99486601-99486629
8	NFIC	chr2:99485503-99486914	ECC-1	luminal epithelium:	n/a	chr2:99486601-99486629
9	GATA3	chr2:99485440-99486871	MCF-7	breast:	n/a	chr2:99486511-99486523
10	SIN3AK20	chr2:99484869-99487036	MCF-7	breast:	n/a	n/a
11	GATA3	chr2:99485632-99486870	MCF-7	breast:	n/a	chr2:99486511-99486523
12	TCF12	chr2:99485436-99486934	ECC-1	luminal epithelium:	n/a	chr2:99486350-99486360

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99485026..99487433-chr2:100105196..100107704,3	MCF-7	breast:
2	chr2:99484412..99487919-chr2:99523957..99528531,6	MCF-7	breast:

Variant related genes	Relation type
KIAA1211L	TF binding region
ENSG00000196872	Chromatin interaction
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1574516	0.82[EUR][1000 genomes]
rs17022036	0.83[EUR][1000 genomes]
rs17022042	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17022046	0.93[ASN][1000 genomes]
rs4571099	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4851161	0.82[CEU][hapmap]
rs4851164	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs4851165	0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs4851166	0.83[EUR][1000 genomes]
rs4851168	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4851169	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs59878807	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs66484268	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67008211	0.81[EUR][1000 genomes]
rs67543009	0.85[EUR][1000 genomes]
rs67650979	0.83[EUR][1000 genomes]
rs67983743	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811067	0.82[EUR][1000 genomes]
rs72811068	0.82[EUR][1000 genomes]
rs72811073	0.82[EUR][1000 genomes]
rs72811074	0.82[EUR][1000 genomes]
rs72811075	0.82[EUR][1000 genomes]
rs72811079	0.82[EUR][1000 genomes]
rs72811084	0.82[EUR][1000 genomes]
rs72811092	0.82[EUR][1000 genomes]
rs72811098	0.82[EUR][1000 genomes]
rs72811102	0.82[EUR][1000 genomes]
rs72813003	0.82[EUR][1000 genomes]
rs72813009	0.82[EUR][1000 genomes]
rs72813012	0.82[EUR][1000 genomes]
rs72813013	0.82[EUR][1000 genomes]
rs72813016	0.82[EUR][1000 genomes]
rs72813021	0.82[EUR][1000 genomes]
rs72957614	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs72958693	0.91[ASN][1000 genomes]
rs72960707	0.85[EUR][1000 genomes]
rs925884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs925885	0.93[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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99481800-99487000	Weak transcription	Lung	lung
2	chr2:99484000-99489000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:99485000-99488200	Enhancers	Fetal Muscle Leg	muscle
4	chr2:99485200-99487400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:99485200-99487800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:99485400-99487400	Enhancers	Fetal Muscle Trunk	muscle
7	chr2:99485600-99499800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:99485800-99487000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr2:99485800-99488200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr2:99485800-99491800	Weak transcription	Brain Anterior Caudate	brain
11	chr2:99486000-99487600	Enhancers	Fetal Thymus	thymus
12	chr2:99486000-99488600	Weak transcription	Right Atrium	heart
13	chr2:99486200-99487000	Enhancers	HMEC	breast
14	chr2:99486200-99487600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr2:99486200-99487800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr2:99486200-99489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:99486400-99487000	Weak transcription	Gastric	stomach
18	chr2:99486400-99487200	Enhancers	Fetal Intestine Large	intestine
19	chr2:99486400-99487400	Enhancers	Fetal Intestine Small	intestine
20	chr2:99486400-99487800	Enhancers	Stomach Mucosa	stomach
21	chr2:99486400-99488000	Enhancers	Esophagus	oesophagus
22	chr2:99486400-99489600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:99486600-99487000	Enhancers	Hela-S3	cervix
24	chr2:99486600-99487600	Enhancers	Pancreas	Pancrea
25	chr2:99486600-99487600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr2:99486600-99489400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:99486600-99489800	Weak transcription	NHEK	skin
28	chr2:99486800-99487000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:99486800-99487000	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr2:99486800-99487400	Enhancers	Colonic Mucosa	Colon
31	chr2:99486800-99489600	Weak transcription	Placenta	Placenta
32	chr2:99486800-99491000	Weak transcription	GM12878-XiMat	blood

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