Variant report

Variant	rs9860171
Chromosome Location	chr3:119461929-119461930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr3:119461735-119462152	HCT-116	colon:	n/a	n/a
2	CTCF	chr3:119461920-119462070	HCPEpiC	choroid plexus:	n/a	n/a
3	ZNF384	chr3:119461772-119462169	K562	blood:	n/a	n/a
4	CTCF	chr3:119461820-119461970	MCF-7	breast:	n/a	n/a
5	CTCF	chr3:119461920-119462070	HPF	lung:	n/a	n/a
6	CTCF	chr3:119461920-119462070	HBMEC	blood vessel:	n/a	n/a
7	CTCF	chr3:119461820-119461970	HFF-Myc	foreskin:	n/a	n/a
8	RAD21	chr3:119461853-119462098	GM12878	blood:	n/a	n/a
9	CTCF	chr3:119461820-119461970	GM12873	blood:	n/a	n/a
10	RAD21	chr3:119461860-119462165	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:119461900-119462050	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr3:119461840-119461990	GM12864	blood:	n/a	n/a
13	CTCF	chr3:119461920-119462070	HEK293	kidney:	n/a	n/a
14	CTCF	chr3:119461800-119461950	NHEK	skin:	n/a	n/a
15	RAD21	chr3:119461733-119462157	HCT-116	colon:	n/a	n/a
16	CTCF	chr3:119461900-119462050	HPAF	blood vessel:	n/a	n/a
17	CTCF	chr3:119461920-119462070	HRPEpiC	eye:	n/a	n/a
18	CTCF	chr3:119461920-119462070	HRE	kidney:	n/a	n/a
19	CTCF	chr3:119461920-119462070	HFF	foreskin:	n/a	n/a
20	CTCF	chr3:119461800-119461950	GM12871	blood:	n/a	n/a
21	CTCF	chr3:119461920-119462070	GM12864	blood:	n/a	n/a
22	RAD21	chr3:119461839-119462098	SK-N-SH_RA	brain:	n/a	n/a
23	CTCF	chr3:119461920-119462070	K562	blood:	n/a	n/a
24	CTCF	chr3:119461920-119462070	GM12873	blood:	n/a	n/a
25	CTCF	chr3:119461920-119462070	HCT-116	colon:	n/a	n/a
26	CTCF	chr3:119461900-119462050	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr3:119461900-119462050	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr3:119461920-119462070	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr3:119461880-119462030	HA-sp	spinal cord:	n/a	n/a
30	CTCF	chr3:119461920-119462070	HEEpiC	esophagus:	n/a	n/a
31	RAD21	chr3:119461890-119462133	ECC-1	luminal epithelium:	n/a	n/a
32	CTCF	chr3:119461900-119462050	GM12864	blood:	n/a	n/a
33	RAD21	chr3:119461841-119462256	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr3:119461900-119462050	GM12873	blood:	n/a	n/a
35	CTCF	chr3:119461871-119462145	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr3:119461920-119462070	GM06990	blood:	n/a	n/a
37	RAD21	chr3:119461840-119462130	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr3:119461920-119462070	HepG2	liver:	n/a	n/a
39	RAD21	chr3:119461818-119462127	ECC-1	luminal epithelium:	n/a	n/a
40	CTCF	chr3:119461800-119461950	NHDF-neo	bronchial:	n/a	n/a
41	CTCF	chr3:119461920-119462070	HMF	breast:	n/a	n/a
42	CTCF	chr3:119461863-119462082	K562	blood:	n/a	n/a
43	CTCF	chr3:119461920-119462070	GM12874	blood:	n/a	n/a
44	ZNF384	chr3:119461926-119462067	GM12878	blood:	n/a	n/a
45	CTCF	chr3:119461900-119462050	A549	lung:	n/a	n/a
46	CTCF	chr3:119461900-119462050	Caco-2	colon:	n/a	n/a
47	RAD21	chr3:119461925-119462090	HepG2	liver:	n/a	n/a
48	CTCF	chr3:119461800-119461950	BE2_C	brain:	n/a	n/a

No data

Variant related genes	Relation type
MAATS1	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13316467	1.00[AFR][1000 genomes]
rs13316524	1.00[AFR][1000 genomes]
rs13318819	0.85[AFR][1000 genomes]
rs28370398	1.00[AFR][1000 genomes]
rs28415065	1.00[AFR][1000 genomes]
rs28464044	1.00[AFR][1000 genomes]
rs28484588	1.00[AFR][1000 genomes]
rs28595123	1.00[AFR][1000 genomes]
rs28678836	1.00[AFR][1000 genomes]
rs6795467	1.00[AFR][1000 genomes]
rs7617259	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7618191	0.90[AFR][1000 genomes]
rs9289133	1.00[AFR][1000 genomes]
rs9809148	0.86[AFR][1000 genomes]
rs9810454	1.00[AFR][1000 genomes]
rs9811271	1.00[AFR][1000 genomes]
rs9813490	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9814138	1.00[AFR][1000 genomes]
rs9815987	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9817771	1.00[AFR][1000 genomes]
rs9819218	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9820811	1.00[AFR][1000 genomes]
rs9824097	1.00[AFR][1000 genomes]
rs9834015	0.90[AFR][1000 genomes]
rs9835381	1.00[AFR][1000 genomes]
rs9837808	1.00[AFR][1000 genomes]
rs9842101	1.00[AFR][1000 genomes]
rs9844223	0.90[AFR][1000 genomes]
rs9844543	0.90[AFR][1000 genomes]
rs9847782	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9851058	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9853426	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9856637	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9858328	1.00[AFR][1000 genomes]
rs9859568	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9864160	0.95[AFR][1000 genomes]
rs9865259	1.00[AFR][1000 genomes]
rs9866905	1.00[AFR][1000 genomes]
rs9870607	1.00[AFR][1000 genomes]
rs9875512	1.00[AFR][1000 genomes]
rs9881432	1.00[AFR][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	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119423000-119463000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:119423000-119464400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:119423200-119464200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:119423200-119471600	Weak transcription	Fetal Kidney	kidney
5	chr3:119428800-119469200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:119431200-119470400	Weak transcription	Gastric	stomach
7	chr3:119435400-119478200	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:119436800-119462800	Weak transcription	Pancreas	Pancrea
9	chr3:119450400-119463000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:119450600-119474200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:119451000-119473400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:119451200-119465000	Weak transcription	Fetal Brain Female	brain
13	chr3:119451200-119475200	Weak transcription	Fetal Brain Male	brain
14	chr3:119453200-119462800	Weak transcription	Ovary	ovary
15	chr3:119453600-119463000	Weak transcription	Brain Angular Gyrus	brain
16	chr3:119455200-119470200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:119456200-119470600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:119457600-119472200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:119458400-119462800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:119458400-119470000	Weak transcription	Aorta	Aorta
21	chr3:119458800-119471200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:119459400-119470000	Weak transcription	Brain Substantia Nigra	brain
23	chr3:119459600-119462600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:119459600-119462800	Weak transcription	Brain Anterior Caudate	brain
25	chr3:119459600-119472200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:119460000-119464800	Weak transcription	Fetal Stomach	stomach
27	chr3:119460800-119470600	Weak transcription	Left Ventricle	heart
28	chr3:119461800-119462800	Weak transcription	Spleen	Spleen

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