Variant report

Variant	rs3760659
Chromosome Location	chr19:41769104-41769105
allele	G/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	E2F4	chr19:41769101-41770367	GM12878	blood:	n/a	chr19:41770065-41770076 chr19:41770066-41770074 chr19:41769863-41769875 chr19:41770066-41770078 chr19:41770066-41770075 chr19:41770168-41770177 chr19:41770016-41770026 chr19:41770062-41770077 chr19:41770067-41770074 chr19:41770067-41770074 chr19:41770067-41770074
2	EGR1	chr19:41768918-41769268	K562	blood:	n/a	n/a
3	POU2F2	chr19:41768718-41770350	GM12891	blood:	n/a	chr19:41770072-41770084 chr19:41769995-41770005
4	SP1	chr19:41768794-41770564	GM12878	blood:	n/a	chr19:41770157-41770178 chr19:41769743-41769755 chr19:41770051-41770065 chr19:41769814-41769835 chr19:41769745-41769754 chr19:41770050-41770062
5	SP1	chr19:41768812-41771402	HCT-116	colon:	n/a	chr19:41770157-41770178 chr19:41770908-41770917 chr19:41771123-41771132 chr19:41769743-41769755 chr19:41770714-41770726 chr19:41771119-41771133 chr19:41770051-41770065 chr19:41770903-41770917 chr19:41770906-41770918 chr19:41769814-41769835 chr19:41770716-41770725 chr19:41770902-41770915 chr19:41770907-41770917 chr19:41769745-41769754 chr19:41770907-41770916 chr19:41770050-41770062 chr19:41770714-41770726 chr19:41770715-41770724 chr19:41770906-41770918
6	TCF3	chr19:41768902-41769342	GM12878	blood:	n/a	chr19:41769156-41769169
7	MAX	chr19:41768957-41770333	Hela-S3	cervix:	n/a	chr19:41770252-41770262
8	MAFF	chr19:41769010-41769210	K562	blood:	n/a	n/a
9	ATF2	chr19:41768854-41770487	GM12878	blood:	n/a	n/a
10	RELA	chr19:41768979-41770451	GM18505	blood:	n/a	n/a
11	POLR2A	chr19:41768093-41771218	Raji	blood:	n/a	n/a
12	PAX5	chr19:41768913-41769304	GM12878	blood:	n/a	n/a
13	TAF1	chr19:41768951-41769858	H1-hESC	embryonic stem cell:	n/a	n/a
14	PAX5	chr19:41768836-41770310	GM12878	blood:	n/a	n/a
15	EP300	chr19:41768903-41770371	K562	blood:	n/a	chr19:41770071-41770087
16	BATF	chr19:41768958-41769311	GM12878	blood:	n/a	n/a
17	MAX	chr19:41769005-41769196	H1-hESC	embryonic stem cell:	n/a	n/a
18	NFATC1	chr19:41768875-41769845	GM12878	blood:	n/a	n/a
19	GABPA	chr19:41768947-41771242	A549	lung:	n/a	n/a
20	TCF12	chr19:41768850-41769770	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:41768085-41771893	GM19193	blood:	n/a	n/a
22	TBP	chr19:41768989-41772071	K562	blood:	n/a	n/a
23	MTA3	chr19:41768794-41771880	GM12878	blood:	n/a	n/a
24	MYC	chr19:41768923-41771027	K562	blood:	n/a	chr19:41770252-41770262
25	MYC	chr19:41768970-41771026	K562	blood:	n/a	chr19:41770252-41770262
26	RFX5	chr19:41768867-41771382	SK-N-SH	brain:	n/a	chr19:41769824-41769833 chr19:41770167-41770176
27	JUND	chr19:41768915-41772213	A549	lung:	n/a	chr19:41770714-41770723 chr19:41769880-41769889 chr19:41769949-41769961 chr19:41770306-41770315 chr19:41770166-41770175 chr19:41769082-41769093
28	BHLHE40	chr19:41768890-41770683	GM12878	blood:	n/a	n/a
29	FOS	chr19:41768878-41769256	MCF10A-Er-Src	breast:	n/a	chr19:41769082-41769093
30	POLR2A	chr19:41767388-41771764	U87	brain:	n/a	n/a
31	POLR2A	chr19:41768726-41771510	H1-hESC	embryonic stem cell:	n/a	n/a
32	TCF7L2	chr19:41768959-41770411	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr19:41768106-41771857	GM18505	blood:	n/a	n/a
34	POLR2A	chr19:41768798-41772064	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr19:41768901-41770598	HepG2	liver:	n/a	n/a
36	POLR2A	chr19:41767678-41771748	Hela-S3	cervix:	n/a	n/a
37	YY1	chr19:41768901-41771505	A549	lung:	n/a	chr19:41770267-41770276 chr19:41770722-41770733 chr19:41770274-41770282 chr19:41770270-41770282 chr19:41770271-41770281 chr19:41770262-41770276 chr19:41771123-41771134 chr19:41770271-41770293 chr19:41770712-41770726
38	POLR2A	chr19:41767844-41772185	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr19:41768821-41771388	HL-60	blood:	n/a	n/a
40	POLR2A	chr19:41768821-41769885	SK-N-MC	brain:	n/a	n/a
41	POLR2A	chr19:41768047-41772143	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr19:41768868-41770850	MCF-7	breast:	n/a	chr19:41770252-41770262
43	TAF1	chr19:41769031-41771145	SK-N-SH	brain:	n/a	n/a
44	TAF1	chr19:41768963-41769318	GM12892	blood:	n/a	n/a
45	PAX5	chr19:41768901-41770358	GM12878	blood:	n/a	n/a
46	RCOR1	chr19:41768981-41769759	K562	blood:	n/a	n/a
47	RELA	chr19:41769005-41770469	GM19099	blood:	n/a	n/a
48	GABPA	chr19:41768996-41770547	SK-N-SH	brain:	n/a	n/a
49	MAX	chr19:41768815-41771564	A549	lung:	n/a	chr19:41770252-41770262
50	CHD1	chr19:41768973-41769843	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41698019..41700083-chr19:41767122..41769558,2	K562	blood:
2	chr15:90118449..90118990-chr19:41768914..41769517,2	Hela-S3	cervix:
3	chr19:41766631..41773289-chr19:41812153..41817614,9	K562	blood:
4	chr19:41703762..41708765-chr19:41768363..41772371,6	MCF-7	breast:
5	chr19:41766963..41771332-chr19:41813075..41817628,7	K562	blood:
6	chr19:41254948..41257942-chr19:41767479..41769277,2	MCF-7	breast:
7	chr1:153642655..153643489-chr19:41769104..41769856,2	Hela-S3	cervix:
8	chr11:62608913..62609655-chr19:41768905..41769666,2	Hela-S3	cervix:
9	chr19:41730545..41733193-chr19:41768273..41769945,2	MCF-7	breast:
10	chr19:41220377..41222544-chr19:41768201..41769798,2	MCF-7	breast:
11	chr19:41768451..41772660-chr19:41814640..41817683,6	MCF-7	breast:
12	chr19:41767589..41772847-chr19:41812402..41817981,15	MCF-7	breast:
13	chr19:41768995..41769868-chr6:109416228..109417002,2	HCT-116	colon:
14	chr19:41697323..41700714-chr19:41769063..41770894,3	K562	blood:
15	chr19:41766877..41771286-chr19:41856641..41860631,6	K562	blood:
16	chr19:41768247..41770079-chr19:41858302..41861510,3	MCF-7	breast:
17	chr19:41698985..41702051-chr19:41767021..41770015,3	MCF-7	breast:
18	chr19:41729266..41732729-chr19:41766701..41770009,7	K562	blood:
19	chr19:41767651..41769904-chr19:41902855..41905283,2	K562	blood:

Variant related genes	Relation type
HNRNPUL1	TF binding region
ENSG00000167601	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000140534	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000077348	Chromatin interaction
ENSG00000167600	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000188493	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	1.00[CHB][hapmap];0.83[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];0.86[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[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];0.95[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	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12984160	0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12985162	0.89[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12985339	0.94[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1946612	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]
rs1946613	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs2053086	0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2241718	0.89[CHB][hapmap];0.83[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];0.87[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs2304232	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];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]
rs3760660	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs3786556	0.81[ASN][1000 genomes]
rs4591267	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];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];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7256873	0.81[ASN][1000 genomes]
rs8103839	0.94[CHB][hapmap];0.87[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
rs3760659	BAX	cis	cerebellum	SCAN
rs3760659	PSG8	cis	parietal	SCAN
rs3760659	KCNJ14	cis	parietal	SCAN
rs3760659	SLC1A5	cis	parietal	SCAN
rs3760659	PSG2	cis	parietal	SCAN
rs3760659	SLC6A16	cis	cerebellum	SCAN
rs3760659	FOSB	cis	parietal	SCAN
rs3760659	SLC1A5	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41767200-41770400	Active TSS	Brain Germinal Matrix	brain
2	chr19:41767400-41772400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:41767600-41769400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:41767600-41769400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:41767600-41770600	Active TSS	Fetal Brain Female	brain
6	chr19:41767600-41771400	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr19:41767600-41771400	Active TSS	Fetal Stomach	stomach
8	chr19:41767600-41771800	Active TSS	Right Ventricle	heart
9	chr19:41767600-41772200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:41767600-41772200	Active TSS	Psoas Muscle	Psoas
11	chr19:41767600-41772400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr19:41767600-41772400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr19:41767800-41769400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:41767800-41769600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr19:41767800-41769600	Active TSS	Fetal Heart	heart
16	chr19:41767800-41771200	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr19:41767800-41771200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:41767800-41771400	Active TSS	Primary T cells from cord blood	blood
19	chr19:41767800-41771400	Active TSS	Brain Angular Gyrus	brain
20	chr19:41767800-41771400	Active TSS	Colon Smooth Muscle	Colon
21	chr19:41767800-41771800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:41767800-41771800	Active TSS	Fetal Kidney	kidney
23	chr19:41767800-41772000	Active TSS	Aorta	Aorta
24	chr19:41767800-41772200	Active TSS	Esophagus	oesophagus
25	chr19:41767800-41772200	Active TSS	Lung	lung
26	chr19:41767800-41772400	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr19:41767800-41772400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr19:41767800-41772400	Active TSS	Right Atrium	heart
29	chr19:41767800-41772600	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr19:41767800-41773200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr19:41768000-41769600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr19:41768000-41770400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:41768000-41770400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:41768000-41770400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:41768000-41771200	Active TSS	Colonic Mucosa	Colon
36	chr19:41768000-41771400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:41768000-41771400	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:41768000-41771400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr19:41768000-41771600	Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr19:41768000-41771600	Active TSS	Placenta	Placenta
41	chr19:41768000-41771600	Active TSS	Left Ventricle	heart
42	chr19:41768000-41771600	Active TSS	Rectal Smooth Muscle	rectum
43	chr19:41768000-41771600	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr19:41768000-41771800	Active TSS	Fetal Intestine Large	intestine
45	chr19:41768000-41772000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr19:41768000-41772000	Active TSS	Gastric	stomach
47	chr19:41768000-41772200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:41768000-41772200	Active TSS	Ovary	ovary
49	chr19:41768000-41772400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr19:41768000-41772400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links