Variant report

Variant	rs1800652
Chromosome Location	chr9:71661116-71661117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:71660830-71661165	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:71661107-71661157	HIPEpiC	eye:	n/a
2	chr9:71661107-71661157	ECC-1	luminal epithelium:	n/a
3	chr9:71661107-71661157	GM06990	blood:	n/a
4	chr9:71661107-71661157	GM12891	blood:	n/a
5	chr9:71661107-71661157	HRE	kidney:	n/a
6	chr9:71661107-71661157	PFSK-1	brain:	n/a
7	chr9:71661107-71661157	Hepatocyte	liver:	n/a
8	chr9:71661107-71661157	PANC-1	pancreas:	n/a
9	chr9:71661107-71661157	BJ	skin:	n/a
10	chr9:71661107-71661157	SAEC	small airway:	n/a
11	chr9:71661107-71661157	HUVEC	blood vessel:	n/a
12	chr9:71661107-71661157	A549	lung:	n/a
13	chr9:71661107-71661157	AG09309	skin:	n/a
14	chr9:71661107-71661157	SK-N-MC	brain:	n/a
15	chr9:71661107-71661157	HepG2	liver:	n/a
16	chr9:71661107-71661157	GM19239	blood:	n/a
17	chr9:71661107-71661157	T-47D	breast:	n/a
18	chr9:71661107-71661157	BE2_C	brain:	n/a
19	chr9:71661107-71661157	H1-hESC	embryonic stem cell:	embryo
20	chr9:71661107-71661157	AG04449	skin:	fetal
21	chr9:71661107-71661157	HRPEpiC	eye:	n/a
22	chr9:71661107-71661157	HEEpiC	esophagus:	n/a
23	chr9:71661107-71661157	HRCEpiC	kidney:	n/a
24	chr9:71661107-71661157	HNPCEpiC	eye:	n/a
25	chr9:71661107-71661157	U87	brain:	n/a
26	chr9:71661107-71661157	Hela-S3	cervix:	n/a
27	chr9:71661107-71661157	AG10803	skin:	n/a
28	chr9:71661107-71661157	Caco-2	colon:	n/a
29	chr9:71661107-71661157	SKMC	muscle:	n/a
30	chr9:71661107-71661157	HPAEpiC	pulmonary alveolar:	n/a
31	chr9:71661107-71661157	ovcar-3	ovarian:	n/a
32	chr9:71661107-71661157	NB4	blood:	n/a
33	chr9:71661107-71661157	AG09319	gingival:	n/a
34	chr9:71661107-71661157	GM12878	blood:	n/a
35	chr9:71661107-71661157	HCT-116	colon:	n/a
36	chr9:71661107-71661157	K562	blood:	n/a
37	chr9:71661107-71661157	NHDF-neo	bronchial:	n/a
38	chr9:71661107-71661157	SK-N-SH	brain:	n/a
39	chr9:71661107-71661157	NH-A	brain:	n/a
40	chr9:71661107-71661157	HCM	heart:	n/a
41	chr9:71661107-71661157	LNCaP	prostate:	n/a
42	chr9:71661107-71661157	MCF-7	breast:	n/a
43	chr9:71661107-71661157	HAEpiC	amniotic membrane:	n/a
44	chr9:71661107-71661157	NHBE	bronchial:	n/a
45	chr9:71661107-71661157	CMK	blood:	n/a
46	chr9:71661107-71661157	HL-60	blood:	n/a
47	chr9:71661107-71661157	MCF10A-Er-Src	breast:	n/a
48	chr9:71661107-71661157	AoSMC	blood vessel:	n/a
49	chr9:71661107-71661157	HEK293	kidney:	embryo
50	chr9:71661107-71661157	GM12892	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71649461..71652506-chr9:71658685..71662535,4	MCF-7	breast:

No data

Variant related genes	Relation type
FXN	TF binding region
FXN	CpG island
ENSG00000165060	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11145103	0.84[ASN][1000 genomes]
rs12343153	0.99[ASN][1000 genomes]
rs2498428	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9411179	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
13	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer 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
14	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS 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 target site	25 gene(s)	inside rSNPs	diseases
16	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
18	nsv466397	chr9:71574757-71843023	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
19	nsv614550	chr9:71574757-71843023	Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
20	nsv1050692	chr9:71578494-71843023	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
21	nsv893416	chr9:71597840-71888601	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
22	nsv1040539	chr9:71600042-71844108	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
23	nsv540149	chr9:71600042-71844108	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
24	nsv949664	chr9:71607398-71842391	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
25	nsv466398	chr9:71612891-71671116	Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer 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	4 gene(s)	inside rSNPs	diseases
26	nsv614551	chr9:71612891-71671116	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv948708	chr9:71632265-71842391	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
28	nsv1037787	chr9:71635338-71807648	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
29	nsv540151	chr9:71635338-71807648	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
30	nsv893426	chr9:71659280-71719618	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71651400-71663800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:71651600-71661800	Weak transcription	Fetal Brain Female	brain
3	chr9:71651800-71661400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:71651800-71661600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr9:71651800-71680600	Weak transcription	HSMMtube	muscle
6	chr9:71652000-71661400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:71652000-71661400	Weak transcription	Esophagus	oesophagus
8	chr9:71652000-71661600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr9:71652000-71661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:71652000-71661600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:71652000-71661600	Weak transcription	Fetal Intestine Large	intestine
12	chr9:71652000-71661800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr9:71652000-71661800	Weak transcription	Brain Anterior Caudate	brain
14	chr9:71652000-71661800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:71652000-71661800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:71652000-71661800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr9:71652000-71661800	Weak transcription	NHEK	skin
18	chr9:71652000-71662000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:71652000-71663000	Weak transcription	Dnd41	blood
20	chr9:71652000-71663600	Weak transcription	Brain Substantia Nigra	brain
21	chr9:71652000-71663600	Weak transcription	A549	lung
22	chr9:71652000-71664000	Weak transcription	HMEC	breast
23	chr9:71652000-71672800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:71652000-71680600	Weak transcription	Brain Angular Gyrus	brain
25	chr9:71652000-71680800	Weak transcription	Primary B cells from cord blood	blood
26	chr9:71652200-71661200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr9:71652200-71661800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr9:71652600-71661400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:71655800-71661400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr9:71656000-71661400	Genic enhancers	HepG2	liver
31	chr9:71656600-71661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:71656600-71669800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr9:71657400-71661200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:71658000-71670200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr9:71658400-71661200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr9:71658400-71665000	Strong transcription	Fetal Stomach	stomach
37	chr9:71659000-71661200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:71659000-71661400	Enhancers	H1 Cell Line	embryonic stem cell
39	chr9:71659000-71661400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr9:71659000-71661600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:71659000-71661800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr9:71659000-71661800	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr9:71659400-71661200	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr9:71659400-71661200	Enhancers	Adipose Nuclei	Adipose
45	chr9:71659400-71661400	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr9:71659600-71661200	Enhancers	Liver	Liver
47	chr9:71659600-71663800	Weak transcription	Aorta	Aorta
48	chr9:71659600-71689800	Weak transcription	Colonic Mucosa	Colon
49	chr9:71659800-71661400	Weak transcription	Fetal Kidney	kidney
50	chr9:71659800-71661400	Weak transcription	Rectal Mucosa Donor 31	rectum

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