Variant report

Variant	rs1946612
Chromosome Location	chr19:41767987-41767988
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	RAD21	chr19:41767936-41768560	HepG2	liver:	n/a	n/a
2	GABPA	chr19:41767793-41768731	A549	lung:	n/a	n/a
3	RAD21	chr19:41767758-41768738	HCT-116	colon:	n/a	n/a
4	ZBTB33	chr19:41767938-41768646	A549	lung:	n/a	n/a
5	RCOR1	chr19:41767967-41768618	GM12878	blood:	n/a	n/a
6	USF1	chr19:41767783-41768701	HCT-116	colon:	n/a	n/a
7	PBX3	chr19:41767872-41768719	A549	lung:	n/a	n/a
8	EP300	chr19:41767798-41768739	A549	lung:	n/a	n/a
9	POLR2A	chr19:41767844-41768481	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr19:41767934-41768482	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr19:41767826-41767997	HepG2	liver:	n/a	n/a
12	TBP	chr19:41767959-41768727	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:41767388-41771764	U87	brain:	n/a	n/a
14	TCF12	chr19:41767768-41768726	A549	lung:	n/a	n/a
15	SIN3AK20	chr19:41767809-41768699	HCT-116	colon:	n/a	n/a
16	POLR2A	chr19:41767678-41771748	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:41767844-41772185	SK-N-MC	brain:	n/a	n/a
18	FOXA1	chr19:41767839-41768721	HepG2	liver:	n/a	n/a
19	SIN3AK20	chr19:41767885-41768794	SK-N-SH	brain:	n/a	n/a
20	PML	chr19:41767871-41771809	GM12878	blood:	n/a	n/a
21	MAZ	chr19:41767177-41772220	IMR90	lung:	n/a	chr19:41768441-41768450 chr19:41768481-41768490 chr19:41771759-41771769 chr19:41768482-41768493 chr19:41770252-41770262
22	EP300	chr19:41767933-41768615	GM12878	blood:	n/a	n/a
23	RUNX3	chr19:41767899-41768728	GM12878	blood:	n/a	n/a
24	MAX	chr19:41767956-41768672	A549	lung:	n/a	chr19:41768441-41768450 chr19:41768481-41768490 chr19:41768482-41768493
25	USF1	chr19:41767778-41768727	A549	lung:	n/a	n/a
26	GATA3	chr19:41767680-41771473	A549	lung:	n/a	chr19:41769052-41769060 chr19:41769485-41769493 chr19:41769049-41769062
27	SMC3	chr19:41767895-41768555	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:41767879-41773979	GM12878	blood:	n/a	n/a
29	CUX1	chr19:41767975-41768546	GM12878	blood:	n/a	n/a
30	CTCF	chr19:41767880-41768030	AG10803	skin:	n/a	n/a
31	TCF12	chr19:41767598-41772879	A549	lung:	n/a	chr19:41771163-41771170
32	ATF3	chr19:41767707-41768748	A549	lung:	n/a	n/a
33	RAD21	chr19:41767753-41768699	A549	lung:	n/a	n/a
34	RAD21	chr19:41767985-41768654	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr19:41767392-41771263	SK-N-SH	brain:	n/a	n/a
36	SIN3AK20	chr19:41767925-41768762	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr19:41767822-41768699	SK-N-SH	brain:	n/a	n/a
38	SIN3AK20	chr19:41767289-41770705	A549	lung:	n/a	n/a
39	POLR2A	chr19:41767659-41768745	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr19:41766822-41772154	IMR90	lung:	n/a	n/a
41	POLR2A	chr19:41767576-41768812	PANC-1	pancreas:	n/a	n/a
42	EBF1	chr19:41767969-41768623	GM12878	blood:	n/a	chr19:41768343-41768354
43	POLR2A	chr19:41766581-41772173	U87	brain:	n/a	n/a
44	BCL3	chr19:41767315-41771247	A549	lung:	n/a	chr19:41770820-41770833 chr19:41769404-41769417 chr19:41770075-41770084 chr19:41768447-41768460 chr19:41770716-41770725
45	EGR1	chr19:41767964-41768743	HCT-116	colon:	n/a	chr19:41768439-41768452 chr19:41768440-41768454
46	PBX3	chr19:41767666-41768748	SK-N-SH	brain:	n/a	n/a
47	JUND	chr19:41767818-41768768	HCT-116	colon:	n/a	chr19:41768151-41768159
48	POLR2A	chr19:41767865-41770891	PFSK-1	brain:	n/a	n/a
49	FOSL2	chr19:41767461-41772092	A549	lung:	n/a	chr19:41770714-41770723 chr19:41769880-41769889 chr19:41769949-41769961 chr19:41770306-41770315 chr19:41770166-41770175 chr19:41769082-41769093 chr19:41768151-41768159
50	CEBPB	chr19:41767895-41768616	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41753148..41755079-chr19:41765835..41768228,2	MCF-7	breast:
2	chr19:41698019..41700083-chr19:41767122..41769558,2	K562	blood:
3	chr19:41766631..41773289-chr19:41812153..41817614,9	K562	blood:
4	chr19:41766963..41771332-chr19:41813075..41817628,7	K562	blood:
5	chr19:41254948..41257942-chr19:41767479..41769277,2	MCF-7	breast:
6	chr19:41723453..41725082-chr19:41766152..41768338,2	MCF-7	breast:
7	chr19:41767589..41772847-chr19:41812402..41817981,15	MCF-7	breast:
8	chr19:41766877..41771286-chr19:41856641..41860631,6	K562	blood:
9	chr19:41698985..41702051-chr19:41767021..41770015,3	MCF-7	breast:
10	chr19:41729266..41732729-chr19:41766701..41770009,7	K562	blood:
11	chr19:41767651..41769904-chr19:41902855..41905283,2	K562	blood:

Variant related genes	Relation type
HNRNPUL1	TF binding region
ENSG00000255730	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000077348	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000167600	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000167601	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000142046	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1056854	0.82[JPT][hapmap]
rs11466347	0.81[ASN][1000 genomes]
rs11466359	0.81[ASN][1000 genomes]
rs11879429	0.94[ASN][1000 genomes]
rs11879435	0.81[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs11880564	0.86[ASN][1000 genomes]
rs11880729	0.94[ASN][1000 genomes]
rs11881940	0.94[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs11881953	0.89[ASN][1000 genomes]
rs11882467	0.89[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs12972266	0.89[ASN][1000 genomes]
rs12972779	0.83[ASN][1000 genomes]
rs12972949	0.96[ASN][1000 genomes]
rs12974420	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12976536	0.89[ASN][1000 genomes]
rs12977563	0.94[ASN][1000 genomes]
rs12978323	0.94[CEU][hapmap];0.85[CHB][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs12980267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12980942	0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12981053	0.88[ASN][1000 genomes]
rs12982872	0.82[ASN][1000 genomes]
rs12983027	0.84[ASN][1000 genomes]
rs12983339	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12984160	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12985162	0.89[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12985339	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1946613	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2053086	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2241718	0.89[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2241719	0.86[ASN][1000 genomes]
rs2241720	0.89[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2304231	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.94[ASN][1000 genomes]
rs2304232	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2304235	0.81[ASN][1000 genomes]
rs34322801	0.86[ASN][1000 genomes]
rs34772093	0.88[ASN][1000 genomes]
rs35310790	0.82[ASN][1000 genomes]
rs35501756	0.86[ASN][1000 genomes]
rs35546772	0.89[ASN][1000 genomes]
rs35812313	0.96[ASN][1000 genomes]
rs3760659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760660	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3786556	0.81[ASN][1000 genomes]
rs4591267	0.91[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4802112	0.89[CEU][hapmap]
rs4802115	0.81[EUR][1000 genomes]
rs4803451	0.80[EUR][1000 genomes]
rs61459202	0.88[ASN][1000 genomes]
rs67744888	0.96[ASN][1000 genomes]
rs7250883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7256873	0.81[ASN][1000 genomes]
rs8103839	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs8105901	0.94[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1946612	FOSB	cis	parietal	SCAN
rs1946612	SLC6A16	cis	cerebellum	SCAN
rs1946612	SLC1A5	cis	parietal	SCAN
rs1946612	KCNJ14	cis	parietal	SCAN
rs1946612	BAX	cis	cerebellum	SCAN
rs1946612	PSG2	cis	parietal	SCAN
rs1946612	SLC1A5	cis	cerebellum	SCAN
rs1946612	PSG8	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41732600-41768800	Weak transcription	Small Intestine	intestine
2	chr19:41755000-41768000	Weak transcription	Gastric	stomach
3	chr19:41758600-41768000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:41764200-41768400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:41764400-41769000	Weak transcription	Spleen	Spleen
6	chr19:41766000-41768000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:41766000-41768000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:41766000-41768000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:41766000-41768000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:41766000-41768000	Weak transcription	Placenta	Placenta
11	chr19:41766000-41768000	Weak transcription	Left Ventricle	heart
12	chr19:41766000-41768000	Weak transcription	Ovary	ovary
13	chr19:41767200-41768000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:41767200-41768200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:41767200-41768200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:41767200-41770400	Active TSS	Brain Germinal Matrix	brain
17	chr19:41767400-41768000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:41767400-41768000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:41767400-41768000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:41767400-41768000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:41767400-41768000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr19:41767400-41768000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr19:41767400-41768000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:41767400-41768000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:41767400-41768000	Flanking Active TSS	Colonic Mucosa	Colon
26	chr19:41767400-41768000	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr19:41767400-41768000	Transcr. at gene 5' and 3'	NH-A	brain
28	chr19:41767400-41768200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:41767400-41768200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:41767400-41768200	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr19:41767400-41768200	Flanking Active TSS	Pancreas	Pancrea
32	chr19:41767400-41768200	Flanking Active TSS	Thymus	Thymus
33	chr19:41767400-41768200	Flanking Active TSS	HMEC	breast
34	chr19:41767400-41768200	Transcr. at gene 5' and 3'	HSMM	muscle
35	chr19:41767400-41768200	Flanking Active TSS	HUVEC	blood vessel
36	chr19:41767400-41768200	Transcr. at gene 5' and 3'	NHEK	skin
37	chr19:41767400-41768400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:41767400-41768800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr19:41767400-41768800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr19:41767400-41768800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:41767400-41772400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:41767600-41768000	Enhancers	Primary B cells from peripheral blood	blood
43	chr19:41767600-41768000	Enhancers	Primary hematopoietic stem cells	blood
44	chr19:41767600-41768000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr19:41767600-41768000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:41767600-41768000	Active TSS	Brain Cingulate Gyrus	brain
47	chr19:41767600-41768000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr19:41767600-41768000	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr19:41767600-41768000	Enhancers	HepG2	liver
50	chr19:41767600-41768000	Flanking Active TSS	HSMMtube	muscle

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