Variant report

Variant	rs2302776
Chromosome Location	chr17:38178149-38178150
allele	A/G
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	FOSL2	chr17:38177540-38178213	A549	lung:	n/a	chr17:38177857-38177865
2	NR2F2	chr17:38177494-38178150	MCF-7	breast:	n/a	n/a
3	NR3C1	chr17:38177530-38178374	A549	lung:	n/a	chr17:38177869-38177885 chr17:38178021-38178035 chr17:38178074-38178088 chr17:38178068-38178094 chr17:38178045-38178063 chr17:38177867-38177888 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178068-38178094 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178015-38178041
4	FOS	chr17:38177628-38178218	MCF10A-Er-Src	breast:	n/a	chr17:38177857-38177865
5	CREB1	chr17:38177638-38178285	A549	lung:	n/a	n/a
6	POLR2A	chr17:38177288-38178792	HUVEC	blood vessel:	n/a	n/a
7	TFAP2A	chr17:38177506-38178555	Hela-S3	cervix:	n/a	chr17:38178536-38178548 chr17:38177881-38177891 chr17:38177881-38177891 chr17:38177881-38177891 chr17:38177879-38177893 chr17:38177879-38177894 chr17:38178536-38178548 chr17:38177881-38177891 chr17:38178536-38178548 chr17:38178536-38178548 chr17:38177879-38177893
8	POLR2A	chr17:38177199-38178865	U87	brain:	n/a	n/a
9	MYC	chr17:38177621-38178457	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr17:38178007-38178284	A549	lung:	n/a	n/a
11	TCF12	chr17:38177365-38178384	A549	lung:	n/a	chr17:38177945-38177955
12	NR3C1	chr17:38177622-38178305	A549	lung:	n/a	chr17:38177869-38177885 chr17:38178021-38178035 chr17:38178074-38178088 chr17:38178068-38178094 chr17:38178045-38178063 chr17:38177867-38177888 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178068-38178094 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178015-38178041
13	NR3C1	chr17:38177532-38178336	A549	lung:	n/a	chr17:38177869-38177885 chr17:38178021-38178035 chr17:38178074-38178088 chr17:38178068-38178094 chr17:38178045-38178063 chr17:38177867-38177888 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178068-38178094 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178015-38178041
14	POLR2A	chr17:38177199-38178884	U87	brain:	n/a	n/a
15	POLR2A	chr17:38177347-38178768	U87	brain:	n/a	n/a
16	SMARCC1	chr17:38177653-38178293	Hela-S3	cervix:	n/a	n/a
17	NR3C1	chr17:38177475-38178405	A549	lung:	n/a	chr17:38177869-38177885 chr17:38178021-38178035 chr17:38178074-38178088 chr17:38178068-38178094 chr17:38178045-38178063 chr17:38177867-38177888 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178068-38178094 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178015-38178041
18	STAT3	chr17:38177635-38178203	MCF10A-Er-Src	breast:	n/a	chr17:38177772-38177780 chr17:38177831-38177843 chr17:38177935-38177947 chr17:38177941-38177953
19	NR3C1	chr17:38177603-38178312	A549	lung:	n/a	chr17:38177869-38177885 chr17:38178021-38178035 chr17:38178074-38178088 chr17:38178068-38178094 chr17:38178045-38178063 chr17:38177867-38177888 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178068-38178094 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178015-38178041
20	POLR2A	chr17:38177771-38178205	MCF10A-Er-Src	breast:	n/a	n/a
21	FOXP2	chr17:38177671-38178174	PFSK-1	brain:	n/a	n/a
22	FOS	chr17:38177526-38178169	MCF10A-Er-Src	breast:	n/a	chr17:38177857-38177865
23	POLR2A	chr17:38177321-38178723	HUVEC	blood vessel:	n/a	n/a
24	FOS	chr17:38177505-38178182	HUVEC	blood vessel:	n/a	chr17:38177857-38177865
25	NR3C1	chr17:38177579-38178284	A549	lung:	n/a	chr17:38177869-38177885 chr17:38178021-38178035 chr17:38178074-38178088 chr17:38178068-38178094 chr17:38178045-38178063 chr17:38177867-38177888 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178068-38178094 chr17:38177869-38177885 chr17:38178068-38178094 chr17:38178015-38178041
26	TFAP2C	chr17:38177552-38178572	Hela-S3	cervix:	n/a	chr17:38177927-38177942 chr17:38177879-38177894
27	POLR2A	chr17:38177564-38178373	HUVEC	blood vessel:	n/a	n/a
28	STAT3	chr17:38177625-38178300	MCF10A-Er-Src	breast:	n/a	chr17:38177772-38177780 chr17:38177831-38177843 chr17:38177935-38177947 chr17:38177941-38177953
29	MYC	chr17:38177571-38178316	MCF10A-Er-Src	breast:	n/a	n/a
30	GATA3	chr17:38177630-38178178	MCF-7	breast:	n/a	n/a
31	JUN	chr17:38177568-38178153	HUVEC	blood vessel:	n/a	chr17:38177857-38177865
32	STAT3	chr17:38177633-38178206	MCF10A-Er-Src	breast:	n/a	chr17:38177772-38177780 chr17:38177831-38177843 chr17:38177935-38177947 chr17:38177941-38177953
33	STAT3	chr17:38177660-38178235	MCF10A-Er-Src	breast:	n/a	chr17:38177772-38177780 chr17:38177831-38177843 chr17:38177935-38177947 chr17:38177941-38177953
34	MAZ	chr17:38177360-38178414	IMR90	lung:	n/a	n/a
35	FOS	chr17:38177657-38178217	MCF10A-Er-Src	breast:	n/a	chr17:38177857-38177865
36	POLR2A	chr17:38177478-38178718	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr17:38177433-38178644	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr17:38177544-38178269	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr17:38177292-38178768	U87	brain:	n/a	n/a
40	CTCF	chr17:38178020-38178170	BJ	skin:	n/a	chr17:38178077-38178085

No.	Distal block	Cell Line	Cell type
1	chr17:38177803..38180808-chr17:38181920..38184987,3	K562	blood:
2	chr17:38175295..38180645-chr17:38181007..38185256,8	MCF-7	breast:
3	chr17:38135295..38137617-chr17:38176453..38178456,2	K562	blood:
4	chr17:38174842..38178903-chr17:38208625..38211251,3	K562	blood:
5	chr17:38177907..38180041-chr17:38332919..38334626,2	MCF-7	breast:
6	chr17:38175071..38177613-chr17:38178105..38180812,3	MCF-7	breast:

Variant related genes	Relation type
MED24	TF binding region
ENSG00000008838	Chromatin interaction
ENSG00000108344	Chromatin interaction
ENSG00000238793	Chromatin interaction
ENSG00000108352	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11078936	0.95[CHB][hapmap];0.82[CHD][hapmap]
rs11655264	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11658328	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs12309	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs12451547	0.81[ASN][1000 genomes]
rs12451897	0.81[ASN][1000 genomes]
rs12453334	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12453341	0.81[ASN][1000 genomes]
rs12453343	0.81[ASN][1000 genomes]
rs12601929	0.95[CHB][hapmap];0.81[CHD][hapmap]
rs2227319	0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs2227321	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2227333	0.81[ASN][1000 genomes]
rs2241245	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2270401	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2302774	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2302777	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2305481	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2305482	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs25645	0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs4065321	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8066582	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8073254	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs8075668	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9915252	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9916158	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2302776	MED24	cis	cerebellum	SCAN
rs2302776	MED24	cis	parietal	SCAN
rs2302776	KRT222	cis	cerebellum	SCAN
rs2302776	PCGF2	cis	cerebellum	SCAN
rs2302776	GSDMA	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38166800-38178200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:38170000-38178800	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr17:38170400-38181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
6	chr17:38172400-38178400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr17:38173000-38179600	Strong transcription	Fetal Intestine Small	intestine
8	chr17:38173000-38181400	Weak transcription	Fetal Kidney	kidney
9	chr17:38173400-38183800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:38173600-38180200	Genic enhancers	Fetal Muscle Trunk	muscle
12	chr17:38173600-38180400	Genic enhancers	NHLF	lung
13	chr17:38173600-38182000	Strong transcription	Thymus	Thymus
14	chr17:38173800-38179400	Strong transcription	Fetal Intestine Large	intestine
15	chr17:38173800-38179800	Genic enhancers	Spleen	Spleen
16	chr17:38173800-38180600	Strong transcription	Brain Anterior Caudate	brain
17	chr17:38173800-38181400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr17:38173800-38181800	Strong transcription	Primary T cells from cord blood	blood
19	chr17:38173800-38182400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr17:38174000-38178200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:38174200-38179600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:38174200-38180400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:38174200-38180800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr17:38174200-38183200	Strong transcription	Placenta	Placenta
27	chr17:38174200-38183400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:38174200-38183400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:38174200-38187400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr17:38174400-38179200	Strong transcription	Pancreas	Pancrea
31	chr17:38174400-38179800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr17:38174400-38183200	Strong transcription	Primary B cells from peripheral blood	blood
33	chr17:38174400-38193200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr17:38174600-38180400	Genic enhancers	Fetal Muscle Leg	muscle
35	chr17:38174600-38181400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr17:38174600-38181800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr17:38174600-38182000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr17:38174800-38181400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr17:38174800-38192600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr17:38175000-38180600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr17:38175000-38193800	Strong transcription	HepG2	liver
42	chr17:38175200-38181600	Strong transcription	Fetal Thymus	thymus
43	chr17:38175200-38182800	Strong transcription	Brain Angular Gyrus	brain
44	chr17:38175200-38192600	Strong transcription	Fetal Brain Female	brain
45	chr17:38175200-38193200	Strong transcription	Dnd41	blood
46	chr17:38175400-38179800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr17:38175400-38180200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
48	chr17:38175400-38182200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr17:38175400-38188200	Weak transcription	Fetal Heart	heart
50	chr17:38175600-38181800	Weak transcription	Fetal Brain Male	brain

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