Variant report

Variant	rs3129972
Chromosome Location	chr6:30717258-30717259
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	SP1	chr6:30715985-30718315	HCT-116	colon:	n/a	chr6:30716914-30716935 chr6:30716925-30716935 chr6:30716925-30716934
2	JUND	chr6:30716208-30718028	HCT-116	colon:	n/a	chr6:30716903-30716914 chr6:30717571-30717579 chr6:30717470-30717481 chr6:30717569-30717581
3	MYC	chr6:30716740-30718012	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr6:30715116-30717455	HUVEC	blood vessel:	n/a	n/a
5	FOS	chr6:30716813-30717729	MCF10A-Er-Src	breast:	n/a	chr6:30716903-30716914 chr6:30717571-30717579 chr6:30717470-30717481 chr6:30717569-30717581
6	EP300	chr6:30717060-30717737	MCF-7	breast:	n/a	chr6:30717434-30717444
7	MBD4	chr6:30716131-30717537	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:30715860-30718096	HepG2	liver:	n/a	n/a
9	MBD4	chr6:30716036-30718053	HepG2	liver:	n/a	n/a
10	TEAD4	chr6:30716131-30717422	HepG2	liver:	n/a	n/a
11	FOS	chr6:30716720-30717766	MCF10A-Er-Src	breast:	n/a	chr6:30716903-30716914 chr6:30717571-30717579 chr6:30717470-30717481 chr6:30717569-30717581
12	MAX	chr6:30717090-30717760	Hela-S3	cervix:	n/a	n/a
13	NR2F2	chr6:30716812-30717817	MCF-7	breast:	n/a	n/a
14	HDAC2	chr6:30717243-30717795	HepG2	liver:	n/a	chr6:30717434-30717443 chr6:30717710-30717724
15	MAX	chr6:30716877-30717746	A549	lung:	n/a	n/a
16	JUND	chr6:30716667-30717258	HepG2	liver:	n/a	chr6:30716903-30716914
17	FOXA1	chr6:30716618-30717696	HepG2	liver:	n/a	n/a
18	E2F4	chr6:30717175-30717613	MCF10A-Er-Src	breast:	n/a	n/a
19	FOXM1	chr6:30716885-30717745	MCF-7	breast:	n/a	n/a
20	POLR2A	chr6:30716605-30718408	HCT-116	colon:	n/a	n/a
21	POLR2A	chr6:30716649-30717931	Hela-S3	cervix:	n/a	n/a
22	EP300	chr6:30716580-30717663	HepG2	liver:	n/a	chr6:30717434-30717444
23	POLR2A	chr6:30716227-30717299	HepG2	liver:	n/a	n/a
24	BCL3	chr6:30715983-30717583	A549	lung:	n/a	n/a
25	EP300	chr6:30717067-30718205	Hela-S3	cervix:	n/a	chr6:30717434-30717444
26	POLR2A	chr6:30714974-30717727	HUVEC	blood vessel:	n/a	n/a
27	FOXA2	chr6:30716642-30717678	A549	lung:	n/a	n/a
28	POLR2A	chr6:30715731-30717841	HepG2	liver:	n/a	n/a
29	SP1	chr6:30716029-30717518	A549	lung:	n/a	chr6:30716914-30716935 chr6:30716925-30716935 chr6:30716925-30716934
30	JUND	chr6:30716807-30717692	HepG2	liver:	n/a	chr6:30716903-30716914 chr6:30717571-30717579 chr6:30717470-30717481 chr6:30717569-30717581
31	POLR2A	chr6:30715755-30717556	HUVEC	blood vessel:	n/a	n/a
32	MAZ	chr6:30716774-30717734	Hela-S3	cervix:	n/a	n/a
33	NFIC	chr6:30717235-30717800	ECC-1	luminal epithelium:	n/a	n/a
34	TCF12	chr6:30717107-30717844	ECC-1	luminal epithelium:	n/a	n/a
35	HEY1	chr6:30715836-30717970	HepG2	liver:	n/a	n/a
36	NR3C1	chr6:30716756-30717283	A549	lung:	n/a	n/a
37	NR3C1	chr6:30716554-30717309	A549	lung:	n/a	chr6:30716717-30716730 chr6:30716728-30716741
38	NFIC	chr6:30716566-30717712	HepG2	liver:	n/a	n/a
39	TCF12	chr6:30715631-30718180	A549	lung:	n/a	chr6:30716310-30716319
40	SMC3	chr6:30716722-30717310	HepG2	liver:	n/a	n/a
41	ARID3A	chr6:30716761-30717677	HepG2	liver:	n/a	n/a
42	JUND	chr6:30716525-30718018	HCT-116	colon:	n/a	chr6:30716903-30716914 chr6:30717571-30717579 chr6:30717470-30717481 chr6:30717569-30717581
43	GATA3	chr6:30716008-30717883	A549	lung:	n/a	chr6:30716241-30716248 chr6:30716237-30716253 chr6:30716237-30716253 chr6:30716241-30716248 chr6:30716519-30716527 chr6:30717569-30717578 chr6:30716241-30716248 chr6:30716234-30716255 chr6:30716242-30716259
44	FOS	chr6:30716712-30718195	MCF10A-Er-Src	breast:	n/a	chr6:30716903-30716914 chr6:30717571-30717579 chr6:30717470-30717481 chr6:30717569-30717581
45	SP1	chr6:30715846-30717811	A549	lung:	n/a	chr6:30716914-30716935 chr6:30716925-30716935 chr6:30716925-30716934
46	MAX	chr6:30716652-30717779	A549	lung:	n/a	n/a
47	POLR2A	chr6:30715059-30717511	HUVEC	blood vessel:	n/a	n/a
48	MYBL2	chr6:30716126-30718078	HepG2	liver:	n/a	n/a
49	RCOR1	chr6:30717164-30717789	Hela-S3	cervix:	n/a	n/a
50	EP300	chr6:30717092-30717864	ECC-1	luminal epithelium:	n/a	chr6:30717434-30717444

No.	Distal block	Cell Line	Cell type
1	chr6:30715564..30717790-chr6:30842191..30844765,2	K562	blood:
2	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
3	chr6:30717006..30717795-chr6:30758490..30759003,2	MCF-7	breast:
4	chr6:30705171..30717521-chr6:30843972..30856100,74	MCF-7	breast:
5	chr6:30716934..30717878-chr6:30758478..30759255,4	MCF-7	breast:
6	chr6:30704403..30722478-chr6:30842859..30858629,100	MCF-7	breast:
7	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
8	chr6:30715944..30717540-chr6:30787940..30790254,2	K562	blood:

Variant related genes	Relation type
IER3	TF binding region
RN7SL353P	TF binding region
ENSG00000214894	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1059612	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1264351	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1264373	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2524266	0.82[EUR][1000 genomes]
rs3094023	0.90[AMR][1000 genomes]
rs3094118	0.91[EUR][1000 genomes]
rs3094125	0.90[EUR][1000 genomes]
rs3095276	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3095326	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3095327	0.83[EUR][1000 genomes]
rs3095328	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3095332	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3095334	0.89[EUR][1000 genomes]
rs3129973	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3129974	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3129977	0.88[EUR][1000 genomes]
rs3129978	0.89[EUR][1000 genomes]
rs3129980	0.80[EUR][1000 genomes]
rs3129982	0.80[EUR][1000 genomes]
rs3129983	0.80[EUR][1000 genomes]
rs3129984	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3129985	0.80[EUR][1000 genomes]
rs3130117	0.90[AMR][1000 genomes]
rs3130247	0.90[AMR][1000 genomes]
rs3130641	0.83[EUR][1000 genomes]
rs3130658	0.90[EUR][1000 genomes]
rs3130660	0.90[EUR][1000 genomes]
rs3130665	0.91[EUR][1000 genomes]
rs3130668	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130669	0.81[EUR][1000 genomes]
rs3130670	0.85[EUR][1000 genomes]
rs3130673	0.89[EUR][1000 genomes]
rs3131041	0.85[EUR][1000 genomes]
rs3131044	0.80[EUR][1000 genomes]
rs3131045	0.80[EUR][1000 genomes]
rs3131047	0.80[EUR][1000 genomes]
rs3131049	0.80[EUR][1000 genomes]
rs3131050	0.80[EUR][1000 genomes]
rs3131052	0.84[EUR][1000 genomes]
rs3131055	0.80[EUR][1000 genomes]
rs3131058	0.80[EUR][1000 genomes]
rs3131060	0.80[EUR][1000 genomes]
rs3132582	0.83[EUR][1000 genomes]
rs3132583	0.90[EUR][1000 genomes]
rs3132585	0.90[EUR][1000 genomes]
rs3132599	0.89[EUR][1000 genomes]
rs3132600	0.93[EUR][1000 genomes]
rs3132603	0.89[EUR][1000 genomes]
rs3132605	0.89[EUR][1000 genomes]
rs3132610	0.81[AMR][1000 genomes]
rs9262126	0.89[EUR][1000 genomes]
rs9262130	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9262132	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9262135	0.89[EUR][1000 genomes]
rs9262141	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9262142	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9262143	0.85[EUR][1000 genomes]
rs9262146	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9262200	0.80[EUR][1000 genomes]
rs9262202	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers 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	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
9	nsv884101	chr6:30695920-30733121	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	163 gene(s)	inside rSNPs	diseases
10	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
11	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
12	nsv884102	chr6:30706013-30720567	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases
13	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
14	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3129972	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30712200-30719800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:30712600-30719400	Weak transcription	Brain Anterior Caudate	brain
3	chr6:30712600-30719400	Weak transcription	Psoas Muscle	Psoas
4	chr6:30712600-30719600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr6:30712600-30719600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:30712600-30724000	Enhancers	HMEC	breast
7	chr6:30712800-30717600	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr6:30712800-30718400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:30712800-30719400	Weak transcription	Right Ventricle	heart
10	chr6:30712800-30720000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:30713000-30717600	Weak transcription	Adipose Nuclei	Adipose
12	chr6:30713000-30719400	Weak transcription	Fetal Stomach	stomach
13	chr6:30713200-30719200	Weak transcription	Fetal Heart	heart
14	chr6:30713200-30719200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:30714200-30721200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:30714400-30718600	Enhancers	Pancreas	Pancrea
17	chr6:30714800-30719600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:30715000-30718200	Enhancers	Osteobl	bone
19	chr6:30715000-30718600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:30715200-30718000	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr6:30715200-30718200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:30715200-30718200	Enhancers	HSMM	muscle
23	chr6:30715200-30718200	Enhancers	NHDF-Ad	bronchial
24	chr6:30715200-30718400	Flanking Active TSS	HepG2	liver
25	chr6:30715200-30718600	Enhancers	NH-A	brain
26	chr6:30715200-30719400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:30715200-30719800	Enhancers	Fetal Intestine Small	intestine
28	chr6:30715200-30720000	Enhancers	Colonic Mucosa	Colon
29	chr6:30715200-30720800	Enhancers	Fetal Intestine Large	intestine
30	chr6:30715200-30722200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:30715400-30717800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:30715400-30717800	Enhancers	Esophagus	oesophagus
33	chr6:30715400-30718000	Enhancers	Stomach Smooth Muscle	stomach
34	chr6:30715400-30718200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr6:30715600-30717600	Enhancers	K562	blood
36	chr6:30715600-30721600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:30715800-30717600	Enhancers	Fetal Muscle Leg	muscle
38	chr6:30715800-30717800	Enhancers	Right Atrium	heart
39	chr6:30715800-30718000	Flanking Active TSS	NHEK	skin
40	chr6:30716000-30717800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:30716000-30717800	Enhancers	Spleen	Spleen
42	chr6:30716000-30718200	Enhancers	Colon Smooth Muscle	Colon
43	chr6:30716000-30718200	Flanking Active TSS	A549	lung
44	chr6:30716000-30719200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:30716200-30718000	Enhancers	HSMMtube	muscle
46	chr6:30716400-30717600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:30716400-30717600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:30716400-30717800	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr6:30716400-30717800	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr6:30716400-30717800	Enhancers	Fetal Lung	lung

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