Variant report

Variant	rs6417043
Chromosome Location	chr18:6729046-6729047
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	chr18:6729007-6729143	HUVEC	blood vessel:	n/a	n/a
2	MAX	chr18:6729020-6730259	H1-hESC	embryonic stem cell:	n/a	chr18:6729601-6729611
3	SIN3A	chr18:6729002-6730142	H1-hESC	embryonic stem cell:	n/a	chr18:6729730-6729741 chr18:6729718-6729731
4	JUND	chr18:6728927-6730162	H1-hESC	embryonic stem cell:	n/a	chr18:6728931-6728940
5	REST	chr18:6728701-6730477	H1-neurons	neurons:	n/a	chr18:6729715-6729728 chr18:6729711-6729731
6	E2F6	chr18:6728839-6730248	K562	blood:	n/a	chr18:6729600-6729609 chr18:6729725-6729734
7	POLR2A	chr18:6728885-6730175	H1-hESC	embryonic stem cell:	n/a	n/a
8	STAT3	chr18:6729031-6729342	MCF10A-Er-Src	breast:	n/a	chr18:6729119-6729127 chr18:6729267-6729281 chr18:6729170-6729182
9	RAD21	chr18:6729009-6729317	IMR90	lung:	n/a	n/a
10	POLR2A	chr18:6728941-6730271	U87	brain:	n/a	n/a
11	TAL1	chr18:6729012-6729080	K562	blood:	n/a	n/a
12	ZNF263	chr18:6728746-6730123	HEK293-T-REx	kidney:	n/a	chr18:6728824-6728833
13	ZNF384	chr18:6728819-6730093	K562	blood:	n/a	n/a
14	RAD21	chr18:6728907-6730184	H1-hESC	embryonic stem cell:	n/a	n/a
15	RAD21	chr18:6729020-6729311	Hela-S3	cervix:	n/a	n/a
16	UBTF	chr18:6728942-6729128	K562	blood:	n/a	n/a
17	MAZ	chr18:6728769-6730272	IMR90	lung:	n/a	chr18:6729601-6729611
18	POLR2A	chr18:6728653-6730345	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr18:6728829-6730163	K562	blood:	n/a	n/a
20	CTCF	chr18:6728740-6729391	K562	blood:	n/a	chr18:6729229-6729242
21	MAX	chr18:6729040-6730182	K562	blood:	n/a	chr18:6729601-6729611
22	POLR2A	chr18:6728912-6730235	HUVEC	blood vessel:	n/a	n/a
23	HMGN3	chr18:6728713-6730134	K562	blood:	n/a	n/a
24	JUND	chr18:6728508-6730205	K562	blood:	n/a	chr18:6728931-6728940
25	RAD21	chr18:6729004-6730211	SK-N-SH_RA	brain:	n/a	n/a
26	IRF1	chr18:6728419-6729443	K562	blood:	n/a	chr18:6729194-6729208 chr18:6729182-6729202 chr18:6729186-6729200
27	POLR2A	chr18:6728947-6730271	U87	brain:	n/a	n/a
28	MAZ	chr18:6728890-6730131	Hela-S3	cervix:	n/a	chr18:6729601-6729611
29	ARID3A	chr18:6728394-6729188	K562	blood:	n/a	n/a
30	STAT3	chr18:6729042-6729242	MCF10A-Er-Src	breast:	n/a	chr18:6729119-6729127 chr18:6729170-6729182
31	ZNF143	chr18:6728939-6729386	K562	blood:	n/a	chr18:6729163-6729181
32	POLR2A	chr18:6728839-6730114	K562	blood:	n/a	n/a
33	UBTF	chr18:6728985-6729185	K562	blood:	n/a	n/a
34	POLR2A	chr18:6729011-6730214	H1-neurons	neurons:	n/a	n/a
35	EP300	chr18:6728506-6730047	K562	blood:	n/a	chr18:6728958-6728968 chr18:6729195-6729209 chr18:6729184-6729198 chr18:6729101-6729114 chr18:6729692-6729708 chr18:6729725-6729741 chr18:6729297-6729310 chr18:6728929-6728938 chr18:6729793-6729802
36	CTCF	chr18:6728971-6730360	SK-N-SH	brain:	n/a	chr18:6729229-6729242 chr18:6730067-6730075 chr18:6729959-6729968
37	TAF1	chr18:6728889-6730172	H1-hESC	embryonic stem cell:	n/a	n/a
38	MXI1	chr18:6728715-6730225	IMR90	lung:	n/a	n/a
39	ZMIZ1	chr18:6728951-6730111	K562	blood:	n/a	n/a
40	POLR2A	chr18:6729039-6730167	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr18:6728733-6730187	K562	blood:	n/a	n/a
42	TBP	chr18:6728859-6730125	K562	blood:	n/a	n/a
43	MAX	chr18:6728854-6730217	K562	blood:	n/a	chr18:6729601-6729611
44	IRF1	chr18:6728650-6729923	K562	blood:	n/a	chr18:6729194-6729208 chr18:6729182-6729202 chr18:6729186-6729200
45	TBL1XR1	chr18:6728649-6729149	K562	blood:	n/a	n/a
46	MAFK	chr18:6728829-6729145	K562	blood:	n/a	n/a
47	STAT1	chr18:6728832-6730170	Hela-S3	cervix:	n/a	chr18:6729268-6729279 chr18:6729119-6729127 chr18:6729267-6729281 chr18:6729170-6729182
48	KAP1	chr18:6728909-6729545	U2OS	brain:	n/a	n/a
49	POLR2A	chr18:6728842-6730280	K562	blood:	n/a	n/a
50	CCNT2	chr18:6728692-6730125	K562	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LAMA1-3	chr18:6728833-6729167	XLOC_012748
2	lnc-LAMA1-3	chr18:6728820-6729167	ENSG00000266441.1

Variant related genes	Relation type
ARHGAP28	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10853339	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081256	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11081258	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11081261	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081262	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081263	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081265	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11663818	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11663883	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11876610	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12456109	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12458536	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12458555	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12605298	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956941	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12962460	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381520	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28402892	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28675797	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34146208	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35451382	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4078265	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4605246	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4798486	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4798489	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55847427	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57509765	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506429	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506430	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506431	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506432	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506434	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506438	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6506439	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7227172	0.83[EUR][1000 genomes]
rs7227965	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7228459	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7232028	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7232807	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233049	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233410	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233739	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7235385	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237087	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237204	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7238175	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7239808	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7240348	0.83[EUR][1000 genomes]
rs7242667	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72880705	0.84[EUR][1000 genomes]
rs7504466	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505283	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7506354	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7506610	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7506974	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8084747	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8088863	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8093374	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9952482	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059678	chr18:6155114-6838290	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv916883	chr18:6299209-7244642	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS 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	42 gene(s)	inside rSNPs	diseases
3	nsv1055148	chr18:6527292-6790869	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv543629	chr18:6527292-6790869	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3529901	chr18:6537233-6851509	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3529902	chr18:6537233-6851509	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1063762	chr18:6542534-7382339	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv543630	chr18:6542534-7382339	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1057885	chr18:6598684-6754548	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1060757	chr18:6682974-7051982	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv543631	chr18:6682974-7051982	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv2566842	chr18:6728880-6730366	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6417043	RP11-91I8.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:6728400-6729200	Flanking Active TSS	K562	blood
2	chr18:6728400-6730600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:6728600-6729200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr18:6728600-6729200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr18:6728600-6729200	Flanking Active TSS	HSMM	muscle
6	chr18:6728600-6729200	Flanking Active TSS	NH-A	brain
7	chr18:6728600-6729400	Enhancers	Fetal Heart	heart
8	chr18:6728600-6730600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr18:6728800-6729200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:6728800-6729200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr18:6728800-6729200	Enhancers	Brain Angular Gyrus	brain
12	chr18:6728800-6729200	Enhancers	Esophagus	oesophagus
13	chr18:6728800-6729200	Flanking Active TSS	Fetal Intestine Small	intestine
14	chr18:6728800-6729200	Enhancers	Gastric	stomach
15	chr18:6728800-6729200	Active TSS	Right Atrium	heart
16	chr18:6728800-6729200	Flanking Active TSS	HSMMtube	muscle
17	chr18:6728800-6729200	Flanking Active TSS	HUVEC	blood vessel
18	chr18:6728800-6729200	Active TSS	NHEK	skin
19	chr18:6728800-6729400	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr18:6728800-6729400	Enhancers	Placenta Amnion	Placenta Amnion
21	chr18:6728800-6729600	Enhancers	Fetal Brain Male	brain
22	chr18:6728800-6730000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr18:6728800-6730200	Active TSS	Osteobl	bone
24	chr18:6728800-6730400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr18:6728800-6730400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr18:6728800-6730400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr18:6728800-6730400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr18:6728800-6730600	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr18:6728800-6730600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr18:6728800-6730800	Active TSS	Fetal Muscle Trunk	muscle
31	chr18:6728800-6730800	Active TSS	Stomach Smooth Muscle	stomach
32	chr18:6729000-6729200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr18:6729000-6729200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr18:6729000-6729200	Active TSS	Primary hematopoietic stem cells	blood
35	chr18:6729000-6729200	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr18:6729000-6729200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr18:6729000-6729200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr18:6729000-6729200	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr18:6729000-6729200	Enhancers	Liver	Liver
40	chr18:6729000-6729200	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr18:6729000-6729200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr18:6729000-6729200	Flanking Active TSS	Fetal Stomach	stomach
43	chr18:6729000-6729200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr18:6729000-6729200	Flanking Active TSS	Hela-S3	cervix
45	chr18:6729000-6729200	Flanking Active TSS	NHLF	lung
46	chr18:6729000-6729400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr18:6729000-6729400	Flanking Active TSS	Placenta	Placenta
48	chr18:6729000-6729600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr18:6729000-6729600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr18:6729000-6730000	Active TSS	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links