Variant report

Variant	rs34077848
Chromosome Location	chr6:2449408-2449409
allele	A/C
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	RAD21	chr6:2448782-2449546	HCT-116	colon:	n/a	chr6:2449162-2449181
2	RAD21	chr6:2448842-2449470	A549	lung:	n/a	chr6:2449162-2449181
3	RAD21	chr6:2448775-2449503	IMR90	lung:	n/a	chr6:2449162-2449181
4	MAX	chr6:2449039-2449415	NB4	blood:	n/a	n/a
5	RAD21	chr6:2448700-2449603	HCT-116	colon:	n/a	chr6:2449162-2449181
6	RAD21	chr6:2448911-2449487	MCF-7	breast:	n/a	chr6:2449162-2449181
7	JUND	chr6:2449034-2449610	K562	blood:	n/a	chr6:2449419-2449428
8	CTCF	chr6:2448945-2449433	IMR90	lung:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
9	RAD21	chr6:2448542-2449748	SK-N-SH	brain:	n/a	chr6:2449162-2449181
10	CREB1	chr6:2448918-2449648	H1-hESC	embryonic stem cell:	n/a	chr6:2449417-2449430 chr6:2449417-2449430
11	TCF12	chr6:2448922-2449564	A549	lung:	n/a	n/a
12	SMC3	chr6:2448974-2449428	Hela-S3	cervix:	n/a	n/a
13	ATF1	chr6:2449093-2449530	K562	blood:	n/a	n/a
14	MAX	chr6:2448948-2449572	A549	lung:	n/a	n/a
15	CTCF	chr6:2448915-2449536	HCT-116	colon:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
16	BRCA1	chr6:2449010-2449416	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr6:2448973-2449420	MCF-7	breast:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
18	CTCF	chr6:2448871-2449560	HCT-116	colon:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
19	TBL1XR1	chr6:2449065-2449411	K562	blood:	n/a	n/a
20	RAD21	chr6:2448947-2449443	H1-hESC	embryonic stem cell:	n/a	chr6:2449162-2449181
21	SPI1	chr6:2449098-2449412	HL-60	blood:	n/a	chr6:2449373-2449382
22	KAP1	chr6:2449080-2449593	U2OS	brain:	n/a	n/a
23	RAD21	chr6:2448953-2449409	H1-hESC	embryonic stem cell:	n/a	chr6:2449162-2449181
24	ATF3	chr6:2449106-2449597	K562	blood:	n/a	chr6:2449420-2449427 chr6:2449420-2449428 chr6:2449420-2449430 chr6:2449417-2449430 chr6:2449417-2449427 chr6:2449416-2449429 chr6:2449417-2449427 chr6:2449417-2449430 chr6:2449418-2449429 chr6:2449418-2449431 chr6:2449420-2449431 chr6:2449419-2449427 chr6:2449420-2449430 chr6:2449419-2449430 chr6:2449416-2449431
25	CTCF	chr6:2448773-2449590	A549	lung:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
26	RAD21	chr6:2448864-2449472	MCF-7	breast:	n/a	chr6:2449162-2449181
27	ATF2	chr6:2448968-2449569	H1-hESC	embryonic stem cell:	n/a	n/a
28	SPI1	chr6:2448975-2449570	HL-60	blood:	n/a	chr6:2449373-2449382 chr6:2449542-2449549
29	JUND	chr6:2449074-2449530	H1-hESC	embryonic stem cell:	n/a	chr6:2449419-2449428
30	MAX	chr6:2448903-2449549	HCT-116	colon:	n/a	n/a
31	E2F6	chr6:2449025-2449723	H1-hESC	embryonic stem cell:	n/a	chr6:2449418-2449427 chr6:2449420-2449429
32	CTCF	chr6:2449380-2449530	AG04449	skin:	n/a	n/a
33	UBTF	chr6:2449153-2449438	K562	blood:	n/a	n/a
34	RAD21	chr6:2448877-2449420	ECC-1	luminal epithelium:	n/a	chr6:2449162-2449181
35	CREB1	chr6:2449047-2449623	H1-hESC	embryonic stem cell:	n/a	chr6:2449417-2449430 chr6:2449417-2449430
36	CTCF	chr6:2448894-2449489	MCF-7	breast:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180
37	RAD21	chr6:2448949-2449523	H1-hESC	embryonic stem cell:	n/a	chr6:2449162-2449181
38	RAD21	chr6:2448816-2449415	HepG2	liver:	n/a	chr6:2449162-2449181
39	RAD21	chr6:2448829-2449503	ECC-1	luminal epithelium:	n/a	chr6:2449162-2449181
40	RFX5	chr6:2449375-2449507	K562	blood:	n/a	n/a
41	CTCF	chr6:2448752-2449585	SK-N-SH	brain:	n/a	chr6:2449166-2449179 chr6:2449164-2449182 chr6:2449159-2449180

No.	Distal block	Cell Line	Cell type
1	chr6:2353810..2354693-chr6:2448790..2449627,3	MCF-7	breast:
2	chr6:2209266..2210149-chr6:2448969..2449652,2	MCF-7	breast:
3	chr6:2448902..2449578-chr6:2695787..2696287,2	MCF-7	breast:
4	chr6:2448825..2449584-chr6:2634344..2635312,4	MCF-7	breast:

Variant related genes	Relation type
GMDS-AS1	TF binding region
ENSG00000164385	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13194198	0.82[EUR][1000 genomes]
rs13198172	0.84[EUR][1000 genomes]
rs17135028	0.82[EUR][1000 genomes]
rs17536894	0.86[EUR][1000 genomes]
rs17609498	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2073004	0.82[EUR][1000 genomes]
rs34610626	0.86[EUR][1000 genomes]
rs34854900	0.82[EUR][1000 genomes]
rs34901328	0.86[EUR][1000 genomes]
rs34996746	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35182831	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35658601	0.82[EUR][1000 genomes]
rs35892674	0.86[EUR][1000 genomes]
rs4959184	0.82[EUR][1000 genomes]
rs4959668	0.85[EUR][1000 genomes]
rs4959669	0.84[EUR][1000 genomes]
rs55939357	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56343276	0.86[EUR][1000 genomes]
rs59493792	0.86[EUR][1000 genomes]
rs71552124	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2414600-2452000	Weak transcription	Ovary	ovary
2	chr6:2417600-2454200	Weak transcription	Pancreas	Pancrea
3	chr6:2448400-2450000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:2448600-2449600	Enhancers	Duodenum Mucosa	Duodenum
5	chr6:2448600-2449800	Enhancers	Fetal Brain Male	brain
6	chr6:2448600-2451400	Enhancers	Hela-S3	cervix
7	chr6:2448800-2450000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:2449000-2449600	Active TSS	Brain Angular Gyrus	brain
9	chr6:2449200-2449600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:2449200-2449600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr6:2449200-2449600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:2449200-2449600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:2449200-2449600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:2449200-2449600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr6:2449200-2449600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr6:2449200-2449600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:2449200-2449600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:2449200-2449600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:2449200-2449600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr6:2449200-2449600	Active TSS	Primary B cells from cord blood	blood
21	chr6:2449200-2449600	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:2449200-2449600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr6:2449200-2449600	Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr6:2449200-2449600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:2449200-2449600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:2449200-2449600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:2449200-2449600	Active TSS	Muscle Satellite Cultured Cells	--
28	chr6:2449200-2449600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr6:2449200-2449600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:2449200-2449600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:2449200-2449600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:2449200-2449600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:2449200-2449600	Enhancers	Adipose Nuclei	Adipose
34	chr6:2449200-2449600	Active TSS	Aorta	Aorta
35	chr6:2449200-2449600	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr6:2449200-2449600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr6:2449200-2449600	Enhancers	Fetal Brain Female	brain
38	chr6:2449200-2449600	Flanking Active TSS	Fetal Heart	heart
39	chr6:2449200-2449600	Flanking Active TSS	Fetal Intestine Small	intestine
40	chr6:2449200-2449600	Flanking Active TSS	Fetal Kidney	kidney
41	chr6:2449200-2449600	Flanking Active TSS	Fetal Lung	lung
42	chr6:2449200-2449600	Enhancers	Placenta	Placenta
43	chr6:2449200-2449600	Enhancers	Fetal Stomach	stomach
44	chr6:2449200-2449600	Enhancers	Fetal Thymus	thymus
45	chr6:2449200-2449600	Enhancers	Left Ventricle	heart
46	chr6:2449200-2449600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr6:2449200-2449600	Enhancers	Right Atrium	heart
48	chr6:2449200-2449600	Active TSS	Stomach Smooth Muscle	stomach
49	chr6:2449200-2449600	Enhancers	HepG2	liver
50	chr6:2449200-2449600	Flanking Active TSS	HMEC	breast

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