Variant report

Variant	rs6891700
Chromosome Location	chr5:36241643-36241644
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	HDAC2	chr5:36240893-36242672	MCF-7	breast:	n/a	n/a
2	HCFC1	chr5:36239863-36243624	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:36241629-36242629	HCT-116	colon:	n/a	n/a
4	SIN3AK20	chr5:36240739-36242839	MCF-7	breast:	n/a	n/a
5	POLR2A	chr5:36241077-36242751	MCF-7	breast:	n/a	n/a
6	MAZ	chr5:36240902-36243177	Hela-S3	cervix:	n/a	chr5:36242510-36242519 chr5:36241253-36241263 chr5:36242509-36242520 chr5:36242040-36242049 chr5:36242510-36242520 chr5:36242918-36242929 chr5:36242509-36242519 chr5:36242506-36242521 chr5:36242511-36242518 chr5:36242510-36242520 chr5:36242509-36242520 chr5:36242508-36242521 chr5:36242510-36242519 chr5:36242509-36242518 chr5:36241340-36241350
7	MAX	chr5:36240831-36243080	K562	blood:	n/a	chr5:36242510-36242519 chr5:36241253-36241263 chr5:36242509-36242520 chr5:36242040-36242049 chr5:36242510-36242520 chr5:36242918-36242929 chr5:36242509-36242519 chr5:36242506-36242521 chr5:36242511-36242518 chr5:36242510-36242520 chr5:36242509-36242520 chr5:36242508-36242521 chr5:36242510-36242520 chr5:36242510-36242519 chr5:36242509-36242518 chr5:36241340-36241350
8	TCF12	chr5:36240917-36242719	ECC-1	luminal epithelium:	n/a	n/a
9	MXI1	chr5:36240685-36242673	Hela-S3	cervix:	n/a	chr5:36242511-36242520
10	POLR2A	chr5:36241009-36243239	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:36240788-36243082	K562	blood:	n/a	n/a
12	POLR2A	chr5:36240945-36242715	H1-neurons	neurons:	n/a	n/a
13	YY1	chr5:36240944-36242517	K562	blood:	n/a	chr5:36242450-36242461 chr5:36242192-36242214 chr5:36241259-36241268 chr5:36241256-36241265 chr5:36241531-36241545 chr5:36241972-36241986 chr5:36241309-36241320 chr5:36241977-36241986 chr5:36242202-36242214 chr5:36242419-36242428 chr5:36242305-36242319
14	E2F6	chr5:36240991-36243083	K562	blood:	n/a	chr5:36241977-36241986 chr5:36242131-36242143 chr5:36242454-36242465 chr5:36242293-36242302 chr5:36242453-36242465 chr5:36241999-36242014 chr5:36242425-36242435 chr5:36241257-36241267 chr5:36242419-36242428 chr5:36242267-36242279
15	CTCF	chr5:36241429-36242462	IMR90	lung:	n/a	chr5:36241528-36241541 chr5:36242152-36242165
16	MYC	chr5:36240916-36242666	K562	blood:	n/a	chr5:36242510-36242519 chr5:36241253-36241263 chr5:36242509-36242520 chr5:36242040-36242049 chr5:36242510-36242520 chr5:36242509-36242519 chr5:36242506-36242521 chr5:36242511-36242518 chr5:36242510-36242520 chr5:36242509-36242520 chr5:36242508-36242521 chr5:36242510-36242520 chr5:36242510-36242519 chr5:36242509-36242518 chr5:36241340-36241350
17	JUN	chr5:36239412-36243190	K562	blood:	n/a	chr5:36242295-36242304 chr5:36242671-36242680 chr5:36239492-36239501 chr5:36242656-36242665
18	TCF12	chr5:36241629-36242313	GM12878	blood:	n/a	n/a
19	ARID3A	chr5:36241585-36241671	HepG2	liver:	n/a	n/a
20	SMARCB1	chr5:36240887-36243284	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr5:36238945-36242654	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr5:36240938-36242716	H1-neurons	neurons:	n/a	n/a
23	HCFC1	chr5:36240933-36242623	K562	blood:	n/a	n/a
24	EP300	chr5:36240894-36242803	ECC-1	luminal epithelium:	n/a	chr5:36241136-36241152 chr5:36241959-36241972 chr5:36241259-36241268
25	CTCF	chr5:36241500-36241650	NB4	blood:	n/a	chr5:36241528-36241541
26	POLR2A	chr5:36239114-36243772	HepG2	liver:	n/a	n/a
27	TAF1	chr5:36240930-36241709	Hela-S3	cervix:	n/a	n/a
28	SMC3	chr5:36240900-36242572	Hela-S3	cervix:	n/a	chr5:36241546-36241553 chr5:36242272-36242282
29	ZNF143	chr5:36240943-36241695	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr5:36241638-36243083	HepG2	liver:	n/a	chr5:36242510-36242519 chr5:36242509-36242520 chr5:36242040-36242049 chr5:36242510-36242520 chr5:36242918-36242929 chr5:36242509-36242519 chr5:36242506-36242521 chr5:36242511-36242518 chr5:36242510-36242520 chr5:36242509-36242520 chr5:36242508-36242521 chr5:36242510-36242520 chr5:36242510-36242519 chr5:36242509-36242518
31	TAF1	chr5:36240859-36242775	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr5:36241003-36242700	GM12878	blood:	n/a	n/a
33	TBL1XR1	chr5:36241567-36242595	GM12878	blood:	n/a	n/a
34	BHLHE40	chr5:36240908-36242612	K562	blood:	n/a	chr5:36242305-36242321
35	GTF2F1	chr5:36241278-36241667	K562	blood:	n/a	n/a
36	POLR2A	chr5:36240969-36243013	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr5:36240980-36242703	ProgFib	skin:	n/a	n/a
38	ZBTB7A	chr5:36240879-36241789	ECC-1	luminal epithelium:	n/a	chr5:36241533-36241542
39	CREB1	chr5:36241634-36242621	A549	lung:	n/a	n/a
40	E2F1	chr5:36241484-36242638	Hela-S3	cervix:	n/a	chr5:36242453-36242464 chr5:36241977-36241986 chr5:36242131-36242143 chr5:36242293-36242302 chr5:36242453-36242465 chr5:36241999-36242014 chr5:36242425-36242435 chr5:36242419-36242428 chr5:36242267-36242279
41	TAF1	chr5:36240958-36242553	K562	blood:	n/a	n/a
42	MAZ	chr5:36241434-36242753	GM12878	blood:	n/a	chr5:36242510-36242519 chr5:36242509-36242520 chr5:36242040-36242049 chr5:36242510-36242520 chr5:36242509-36242519 chr5:36242506-36242521 chr5:36242511-36242518 chr5:36242510-36242520 chr5:36242509-36242520 chr5:36242508-36242521 chr5:36242510-36242519 chr5:36242509-36242518
43	HMGN3	chr5:36241031-36242719	K562	blood:	n/a	n/a
44	CTCF	chr5:36241426-36242467	K562	blood:	n/a	chr5:36241528-36241541 chr5:36242152-36242165
45	MYC	chr5:36240829-36242973	K562	blood:	n/a	chr5:36242510-36242519 chr5:36241253-36241263 chr5:36242509-36242520 chr5:36242040-36242049 chr5:36242510-36242520 chr5:36242918-36242929 chr5:36242509-36242519 chr5:36242506-36242521 chr5:36242511-36242518 chr5:36242510-36242520 chr5:36242509-36242520 chr5:36242508-36242521 chr5:36242510-36242520 chr5:36242510-36242519 chr5:36242509-36242518 chr5:36241340-36241350
46	TFAP2A	chr5:36240924-36242577	Hela-S3	cervix:	n/a	chr5:36242273-36242284 chr5:36242220-36242231 chr5:36242221-36242229 chr5:36242220-36242231 chr5:36242272-36242284 chr5:36242221-36242229 chr5:36242220-36242231 chr5:36242220-36242231 chr5:36242273-36242284 chr5:36242215-36242230 chr5:36242221-36242229 chr5:36241329-36241340 chr5:36242272-36242287 chr5:36242220-36242231
47	POLR2A	chr5:36241400-36243174	GM12878	blood:	n/a	n/a
48	CHD2	chr5:36241557-36243076	K562	blood:	n/a	n/a
49	MAX	chr5:36240867-36243142	NB4	blood:	n/a	chr5:36242510-36242519 chr5:36241253-36241263 chr5:36242509-36242520 chr5:36242040-36242049 chr5:36242510-36242520 chr5:36242918-36242929 chr5:36242509-36242519 chr5:36242506-36242521 chr5:36242511-36242518 chr5:36242510-36242520 chr5:36242509-36242520 chr5:36242508-36242521 chr5:36242510-36242520 chr5:36242510-36242519 chr5:36242509-36242518 chr5:36241340-36241350
50	POLR2A	chr5:36240909-36242659	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:129939337..129940255-chr5:36241535..36242514,2	NB4	blood:
2	chr17:62501974..62502835-chr5:36241044..36242027,2	Hela-S3	cervix:
3	chr11:67272246..67273016-chr5:36240996..36241835,2	Hela-S3	cervix:
4	chr5:36220213..36223106-chr5:36238566..36243203,4	K562	blood:
5	chr4:129208497..129209007-chr5:36241002..36241648,2	NB4	blood:
6	chr5:36241118..36241801-chr6:26156530..26157189,2	Hela-S3	cervix:
7	chr5:36217513..36219100-chr5:36239922..36242723,2	MCF-7	breast:
8	chr5:36241537..36242362-chr6:32939583..32940246,2	Hela-S3	cervix:
9	chr16:56965897..56966608-chr5:36241516..36242437,2	Hela-S3	cervix:
10	chr1:249131837..249132700-chr5:36241166..36241931,2	Hela-S3	cervix:
11	chr5:36205557..36207840-chr5:36241465..36243259,2	MCF-7	breast:
12	chr14:51410974..51411953-chr5:36241280..36242185,2	Hela-S3	cervix:
13	chr5:36150463..36155255-chr5:36239958..36244873,10	K562	blood:
14	chr5:36150467..36154483-chr5:36238242..36244873,13	K562	blood:
15	chr19:45927158..45928031-chr5:36241578..36242532,2	Hela-S3	cervix:
16	chr17:80055721..80056463-chr5:36241598..36242471,2	Hela-S3	cervix:
17	chr13:99852232..99853002-chr5:36241181..36242000,2	Hela-S3	cervix:
18	chr1:155225189..155225823-chr5:36241537..36242100,2	Hela-S3	cervix:
19	chr5:36241334..36243447-chr6:24720553..24722359,2	K562	blood:
20	chr12:7053207..7053942-chr5:36241584..36242527,2	Hela-S3	cervix:

Variant related genes	Relation type
NADK2	TF binding region
ENSG00000112308	Chromatin interaction
ENSG00000152620	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000051108	Chromatin interaction
ENSG00000164040	Chromatin interaction
ENSG00000272173	Chromatin interaction
ENSG00000171161	Chromatin interaction
ENSG00000164187	Chromatin interaction
ENSG00000245711	Chromatin interaction
ENSG00000145604	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000201223	Chromatin interaction
ENSG00000084234	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000110697	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000228889	Chromatin interaction
ENSG00000160767	Chromatin interaction
ENSG00000100504	Chromatin interaction
ENSG00000012061	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000169710	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10035473	0.87[AMR][1000 genomes]
rs57097362	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830262	chr5:36074311-36293872	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	63 gene(s)	inside rSNPs	diseases
2	nsv1015638	chr5:36203646-36312576	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36239800-36242600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:36239800-36242800	Active TSS	NHLF	lung
3	chr5:36240000-36242800	Active TSS	Ovary	ovary
4	chr5:36240000-36242800	Active TSS	Right Atrium	heart
5	chr5:36240200-36242400	Active TSS	Fetal Muscle Leg	muscle
6	chr5:36240200-36242800	Active TSS	Aorta	Aorta
7	chr5:36240200-36242800	Active TSS	Psoas Muscle	Psoas
8	chr5:36240200-36243200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:36240400-36242200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr5:36240400-36242400	Active TSS	Fetal Muscle Trunk	muscle
11	chr5:36240400-36242400	Active TSS	K562	blood
12	chr5:36240400-36242600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:36240400-36242600	Active TSS	Fetal Intestine Large	intestine
14	chr5:36240400-36242800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:36240400-36242800	Active TSS	Colon Smooth Muscle	Colon
16	chr5:36240400-36242800	Active TSS	Right Ventricle	heart
17	chr5:36240400-36243000	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr5:36240400-36243200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:36240600-36242400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:36240600-36242600	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr5:36240600-36242600	Active TSS	HepG2	liver
22	chr5:36240600-36242600	Active TSS	NHDF-Ad	bronchial
23	chr5:36240600-36242800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:36240600-36242800	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr5:36240600-36242800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr5:36240600-36242800	Active TSS	Brain Substantia Nigra	brain
27	chr5:36240600-36242800	Active TSS	Fetal Brain Female	brain
28	chr5:36240600-36242800	Active TSS	Fetal Kidney	kidney
29	chr5:36240600-36242800	Active TSS	Left Ventricle	heart
30	chr5:36240600-36243200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:36240600-36243200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:36240600-36243200	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr5:36240600-36243200	Active TSS	Small Intestine	intestine
34	chr5:36240800-36241800	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr5:36240800-36242200	Active TSS	Fetal Heart	heart
36	chr5:36240800-36242400	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr5:36240800-36242400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:36240800-36242400	Active TSS	Fetal Stomach	stomach
39	chr5:36240800-36242400	Active TSS	Placenta Amnion	Placenta Amnion
40	chr5:36240800-36242600	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr5:36240800-36242600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:36240800-36242600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:36240800-36242600	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr5:36240800-36242600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:36240800-36242600	Active TSS	Stomach Smooth Muscle	stomach
46	chr5:36240800-36242600	Active TSS	HSMMtube	muscle
47	chr5:36240800-36242800	Active TSS	H1 Cell Line	embryonic stem cell
48	chr5:36240800-36242800	Active TSS	H9 Cell Line	embryonic stem cell
49	chr5:36240800-36242800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:36240800-36242800	Active TSS	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links