Variant report

Variant	rs6576996
Chromosome Location	chr2:97623312-97623313
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	TCF12	chr2:97623120-97623412	H1-hESC	embryonic stem cell:	n/a	chr2:97623262-97623272 chr2:97623247-97623257
2	SIN3AK20	chr2:97623151-97623421	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr2:97623039-97623503	H1-hESC	embryonic stem cell:	n/a	chr2:97623262-97623271
4	SIN3A	chr2:97623059-97623489	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:97480973..97483903-chr2:97621623..97628750,6	MCF-7	breast:
2	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
3	chr2:97537658..97539492-chr2:97622900..97626326,3	K562	blood:
4	chr2:97302399..97305389-chr2:97622198..97624620,2	K562	blood:
5	chr2:97536159..97540837-chr2:97622900..97627821,5	K562	blood:
6	chr2:97623151..97625255-chr2:97629201..97631510,2	MCF-7	breast:

Variant related genes	Relation type
RNA5SP101	TF binding region
ENSG00000213337	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000114982	Chromatin interaction
ENSG00000168763	Chromatin interaction
ENSG00000163126	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11890407	0.88[EUR][1000 genomes]
rs11891458	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12105727	0.87[CEU][hapmap]
rs17119655	0.90[GIH][hapmap];0.80[MEX][hapmap]
rs59178801	0.82[EUR][1000 genomes]
rs60019075	0.82[EUR][1000 genomes]
rs60608738	0.82[EUR][1000 genomes]
rs6576990	0.80[MEX][hapmap]
rs6717064	0.90[GIH][hapmap];0.80[MEX][hapmap]
rs6721921	0.80[MEX][hapmap]
rs6728642	0.82[EUR][1000 genomes]
rs6731522	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6749086	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73959416	0.82[EUR][1000 genomes]
rs7580504	0.80[EUR][1000 genomes]
rs7584641	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7593754	0.89[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs7594227	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh 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
10	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv1001432	chr2:97591069-97671395	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	esv32727	chr2:97616488-97643975	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6576996		cis	Lymphoblastoid	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97617400-97623400	Enhancers	Fetal Stomach	stomach
2	chr2:97619600-97623400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:97619600-97628400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:97620200-97625600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:97620400-97625000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:97620400-97625200	Weak transcription	Brain Angular Gyrus	brain
7	chr2:97620400-97625200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:97620400-97625200	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:97620400-97625800	Weak transcription	Primary T cells from cord blood	blood
10	chr2:97620400-97625800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:97620400-97629400	Weak transcription	Fetal Intestine Large	intestine
12	chr2:97620600-97625200	Weak transcription	Brain Substantia Nigra	brain
13	chr2:97620600-97625600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:97620600-97625600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:97620600-97625600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:97620600-97625600	Weak transcription	Fetal Brain Female	brain
17	chr2:97620600-97626000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:97620600-97626000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:97620600-97628200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:97620800-97625600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:97620800-97625600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:97620800-97625600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:97620800-97625600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:97620800-97625600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:97620800-97626000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:97620800-97626000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:97620800-97626000	Weak transcription	Stomach Mucosa	stomach
28	chr2:97620800-97627600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:97620800-97629600	Weak transcription	Fetal Intestine Small	intestine
30	chr2:97620800-97643600	Weak transcription	Right Atrium	heart
31	chr2:97621000-97626000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:97621000-97626400	Weak transcription	GM12878-XiMat	blood
33	chr2:97621400-97623400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr2:97621400-97623600	Enhancers	Spleen	Spleen
35	chr2:97621800-97625600	Weak transcription	Colonic Mucosa	Colon
36	chr2:97622000-97623400	Enhancers	Fetal Brain Male	brain
37	chr2:97622000-97625400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:97622000-97625600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr2:97622000-97626000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:97622000-97626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:97622200-97626000	Weak transcription	Ovary	ovary
42	chr2:97622200-97626000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr2:97622600-97623400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:97622600-97623400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:97622800-97623400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:97622800-97623400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr2:97622800-97623400	Bivalent Enhancer	Fetal Muscle Leg	muscle
48	chr2:97622800-97623400	Enhancers	Pancreas	Pancrea
49	chr2:97622800-97623400	Bivalent Enhancer	HepG2	liver
50	chr2:97622800-97623600	Enhancers	H1 Cell Line	embryonic stem cell

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