Variant report

Variant	rs1978340
Chromosome Location	chr2:171670121-171670122
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	POLR2A	chr2:171669667-171676754	H1-neurons	neurons:	n/a	n/a
2	REST	chr2:171670030-171672638	HL-60	blood:	n/a	chr2:171671032-171671045 chr2:171670866-171670875 chr2:171672540-171672553 chr2:171670866-171670886 chr2:171670866-171670886 chr2:171670869-171670882 chr2:171670872-171670886 chr2:171670867-171670885 chr2:171670866-171670886
3	SIN3A	chr2:171669186-171672942	H1-hESC	embryonic stem cell:	n/a	chr2:171670866-171670879 chr2:171672333-171672342 chr2:171670871-171670885 chr2:171672540-171672553
4	CTCF	chr2:171670060-171670210	NHLF	lung:	n/a	n/a
5	CTCF	chr2:171670040-171670190	WI-38	lung:	n/a	n/a
6	REST	chr2:171670020-171670350	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr2:171669237-171676101	H1-neurons	neurons:	n/a	n/a
8	CTCF	chr2:171670040-171670190	AG09319	gingival:	n/a	n/a
9	YY1	chr2:171669714-171670137	H1-hESC	embryonic stem cell:	n/a	chr2:171669939-171669949 chr2:171669938-171669950

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171264048..171266072-chr2:171669517..171671938,2	MCF-7	breast:
2	chr2:171669367..171672253-chr2:171672351..171673917,2	K562	blood:

Variant related genes	Relation type
GAD1	TF binding region
ENSG00000235934	Chromatin interaction
ENSG00000128683	Chromatin interaction
ENSG00000071909	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10168078	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs1065651	0.83[EUR][1000 genomes]
rs10930440	0.81[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes]
rs12464863	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs12472397	0.85[JPT][hapmap]
rs1362488	0.83[EUR][1000 genomes]
rs1420378	0.81[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs1420379	0.83[EUR][1000 genomes]
rs1420381	0.85[JPT][hapmap]
rs17694562	0.83[EUR][1000 genomes]
rs17694708	0.80[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs17751035	0.83[EUR][1000 genomes]
rs17751072	0.83[EUR][1000 genomes]
rs17751234	0.83[EUR][1000 genomes]
rs1894920	0.92[JPT][hapmap]
rs1990653	0.83[EUR][1000 genomes]
rs2287110	0.87[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs2287111	0.81[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap]
rs2356234	0.85[JPT][hapmap]
rs2356236	0.82[EUR][1000 genomes]
rs2883888	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34137349	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34436957	0.83[EUR][1000 genomes]
rs35127716	0.82[EUR][1000 genomes]
rs3762553	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3762556	0.82[EUR][1000 genomes]
rs3791871	0.95[ASN][1000 genomes]
rs3791872	0.95[ASN][1000 genomes]
rs3791878	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668315	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs55693618	0.83[EUR][1000 genomes]
rs55923006	0.83[EUR][1000 genomes]
rs56364811	0.83[EUR][1000 genomes]
rs56989102	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58919807	0.82[EUR][1000 genomes]
rs62168399	0.83[EUR][1000 genomes]
rs62168400	0.83[EUR][1000 genomes]
rs62168401	0.83[EUR][1000 genomes]
rs62168446	0.81[EUR][1000 genomes]
rs62168454	0.95[ASN][1000 genomes]
rs6755814	0.94[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6759584	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs7568115	0.81[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap]
rs7600585	0.81[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1806894	chr2:171651783-171679041	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1978340	NOSTRIN	cis	parietal	SCAN
rs1978340	SP9	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171669200-171670400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:171669200-171670400	Enhancers	K562	blood
3	chr2:171669400-171670200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
4	chr2:171669400-171670400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:171669400-171670600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr2:171669400-171670600	Bivalent Enhancer	Brain Hippocampus Middle	brain
7	chr2:171669400-171670800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:171669400-171670800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
9	chr2:171669400-171670800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
10	chr2:171669400-171670800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
11	chr2:171669600-171670200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
12	chr2:171669600-171670200	Bivalent Enhancer	Brain Substantia Nigra	brain
13	chr2:171669600-171670800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr2:171669600-171670800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:171669600-171670800	Bivalent Enhancer	Fetal Thymus	thymus
16	chr2:171669600-171672000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
17	chr2:171669600-171672000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
18	chr2:171669600-171672200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr2:171669600-171673000	Bivalent/Poised TSS	Fetal Brain Female	brain
20	chr2:171669600-171675400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
21	chr2:171669800-171670200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:171669800-171670200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:171669800-171670200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
24	chr2:171669800-171670600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr2:171669800-171670600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:171669800-171670600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr2:171669800-171670600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:171669800-171670800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:171669800-171672000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
30	chr2:171670000-171670200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:171670000-171670200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:171670000-171670200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:171670000-171670200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:171670000-171670200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
35	chr2:171670000-171670400	Bivalent Enhancer	Primary T cells from cord blood	blood
36	chr2:171670000-171670400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
37	chr2:171670000-171670400	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
38	chr2:171670000-171670400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
39	chr2:171670000-171670600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:171670000-171670600	Enhancers	Gastric	stomach
41	chr2:171670000-171670800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
42	chr2:171670000-171670800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:171670000-171670800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:171670000-171670800	Bivalent Enhancer	Liver	Liver
45	chr2:171670000-171670800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr2:171670000-171671000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr2:171670000-171672000	Bivalent Enhancer	Stomach Smooth Muscle	stomach

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