Variant report

Variant	rs6850727
Chromosome Location	chr4:1323273-1323274
allele	C/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	POLR2A	chr4:1319288-1323843	K562	blood:	n/a	n/a
2	MYC	chr4:1323130-1324229	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr4:1323111-1324215	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1323033..1328941-chr4:1337055..1342245,8	MCF-7	breast:
2	chr4:1283391..1285255-chr4:1323176..1325482,2	MCF-7	breast:

Variant related genes	Relation type
MAEA	TF binding region
ENSG00000163945	Chromatin interaction
ENSG00000090316	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10006789	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10012582	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11726178	0.89[ASN][1000 genomes]
rs11726179	0.89[ASN][1000 genomes]
rs11933854	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11933855	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13137852	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17164682	0.83[ASN][1000 genomes]
rs1882099	0.86[ASN][1000 genomes]
rs2293631	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28418481	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28493051	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28712208	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749456	0.83[ASN][1000 genomes]
rs3856982	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4333131	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974600	0.83[ASN][1000 genomes]
rs5013707	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5019560	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58552306	0.84[ASN][1000 genomes]
rs61073965	0.88[ASN][1000 genomes]
rs6148273	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6852717	0.83[ASN][1000 genomes]
rs73075548	0.85[ASN][1000 genomes]
rs73075553	0.84[ASN][1000 genomes]
rs9990527	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
5	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
6	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	nsv461155	chr4:1203265-1352685	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
10	nsv593281	chr4:1203265-1352685	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
11	nsv593298	chr4:1244267-1342521	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
12	nsv878338	chr4:1277826-1358449	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv878339	chr4:1277826-1363886	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv878340	chr4:1277826-1386570	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
15	nsv878341	chr4:1277826-1391400	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
16	nsv1002635	chr4:1282603-1402761	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
17	nsv878342	chr4:1291337-1363886	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
18	nsv878343	chr4:1291337-1391400	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
19	nsv878344	chr4:1291337-1414684	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
20	nsv878345	chr4:1291337-1563920	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
21	nsv461157	chr4:1300077-1352685	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
22	nsv593301	chr4:1300077-1352685	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
23	nsv878346	chr4:1300077-1363886	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
24	nsv878347	chr4:1300077-1866358	Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
25	nsv878348	chr4:1305269-1386570	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
26	esv1833544	chr4:1305962-1327941	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
27	esv1794294	chr4:1307119-1817474	Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
28	nsv980177	chr4:1317488-1323519	Genic enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
29	nsv878349	chr4:1318132-1363886	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
30	nsv878350	chr4:1320023-1500753	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6850727	CRIPAK	Cis_1M	lymphoblastoid	RTeQTL
rs6850727	MAEA	cis	Nerve Tibial	GTEx
rs6850727	MAEA	cis	Thyroid	GTEx
rs6850727	KIAA1530	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1303600-1339400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:1305000-1327200	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr4:1305200-1326600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:1305200-1330200	Weak transcription	Fetal Heart	heart
5	chr4:1306000-1323400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr4:1309200-1330400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:1313600-1335600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:1314800-1328200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:1314800-1335200	Strong transcription	Dnd41	blood
10	chr4:1315000-1325000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr4:1315000-1335600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:1315200-1323400	Strong transcription	Placenta	Placenta
13	chr4:1315200-1324000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:1315200-1335400	Strong transcription	Fetal Brain Female	brain
15	chr4:1315200-1335600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:1315200-1335600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:1315200-1335600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:1315400-1325200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:1315400-1328400	Strong transcription	Adipose Nuclei	Adipose
20	chr4:1315400-1329400	Strong transcription	Colonic Mucosa	Colon
21	chr4:1315400-1331800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:1315400-1332200	Strong transcription	Fetal Intestine Small	intestine
23	chr4:1315400-1335200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:1315400-1335400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr4:1315400-1335400	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr4:1315600-1325200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:1315600-1325400	Strong transcription	Brain Hippocampus Middle	brain
28	chr4:1315600-1325800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr4:1315600-1328200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr4:1315600-1335400	Strong transcription	Brain Germinal Matrix	brain
31	chr4:1315600-1335600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:1315800-1331800	Strong transcription	Fetal Intestine Large	intestine
33	chr4:1315800-1333400	Strong transcription	Fetal Stomach	stomach
34	chr4:1315800-1335200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:1315800-1335400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr4:1315800-1335600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:1315800-1335600	Strong transcription	Liver	Liver
38	chr4:1316000-1323400	Strong transcription	Brain Anterior Caudate	brain
39	chr4:1316000-1323400	Strong transcription	Colon Smooth Muscle	Colon
40	chr4:1316000-1323600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:1316000-1323800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr4:1316000-1325200	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr4:1317200-1333400	Strong transcription	Pancreas	Pancrea
44	chr4:1317400-1323800	Strong transcription	Brain Cingulate Gyrus	brain
45	chr4:1317400-1324000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:1317800-1328200	Weak transcription	A549	lung
47	chr4:1317800-1329000	Strong transcription	Lung	lung
48	chr4:1317800-1339600	Weak transcription	Right Atrium	heart
49	chr4:1318000-1328200	Weak transcription	Hela-S3	cervix
50	chr4:1318000-1328600	Weak transcription	NHDF-Ad	bronchial

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