Variant report

Variant	rs16835409
Chromosome Location	chr1:153506048-153506049
allele	A/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	ZBTB7A	chr1:153505538-153506136	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr1:153505618-153506744	A549	lung:	n/a	n/a
3	PBX3	chr1:153505314-153506846	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr1:153505534-153506114	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr1:153504001-153509011	U87	brain:	n/a	n/a
6	JUND	chr1:153505713-153507187	Hela-S3	cervix:	n/a	chr1:153506973-153506981 chr1:153506973-153506982 chr1:153506972-153506982 chr1:153506399-153506406 chr1:153506396-153506407 chr1:153506974-153506981
7	POLR2A	chr1:153504109-153508508	A549	lung:	n/a	n/a
8	CTCF	chr1:153505900-153506050	GM12872	blood:	n/a	n/a
9	POLR2A	chr1:153505145-153509494	Hela-S3	cervix:	n/a	n/a
10	SIN3A	chr1:153505296-153506129	H1-hESC	embryonic stem cell:	n/a	n/a
11	ZBTB33	chr1:153505646-153506696	SK-N-SH	brain:	n/a	n/a
12	SP1	chr1:153505368-153506836	A549	lung:	n/a	chr1:153506427-153506437 chr1:153505389-153505398 chr1:153506427-153506436 chr1:153506428-153506437 chr1:153506693-153506702 chr1:153506427-153506436
13	TFAP2C	chr1:153505386-153507077	Hela-S3	cervix:	n/a	n/a
14	MAX	chr1:153505614-153506819	Hela-S3	cervix:	n/a	chr1:153506458-153506465
15	POLR2A	chr1:153505214-153506163	MCF-7	breast:	n/a	n/a
16	POLR2A	chr1:153505307-153509454	Hela-S3	cervix:	n/a	n/a
17	EP300	chr1:153505986-153506786	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr1:153505192-153509569	HCT-116	colon:	n/a	n/a
19	MAZ	chr1:153504643-153509324	IMR90	lung:	n/a	chr1:153506458-153506465 chr1:153508744-153508753 chr1:153506973-153506982 chr1:153509221-153509231 chr1:153506972-153506981 chr1:153509055-153509062 chr1:153508744-153508753
20	MAX	chr1:153505450-153509582	HCT-116	colon:	n/a	chr1:153506458-153506465 chr1:153508744-153508753 chr1:153506973-153506982 chr1:153509221-153509231 chr1:153506972-153506981 chr1:153509055-153509062 chr1:153508744-153508753
21	NFYA	chr1:153505675-153506550	Hela-S3	cervix:	n/a	n/a
22	KAT2A	chr1:153505730-153507273	Hela-S3	cervix:	n/a	n/a
23	CHD2	chr1:153505698-153506056	H1-hESC	embryonic stem cell:	n/a	n/a
24	RAD21	chr1:153505508-153506963	IMR90	lung:	n/a	chr1:153505773-153505792
25	JUND	chr1:153505492-153506847	A549	lung:	n/a	chr1:153506399-153506406 chr1:153506396-153506407
26	CEBPB	chr1:153505401-153506850	A549	lung:	n/a	n/a
27	GATA2	chr1:153505685-153506558	HUVEC	blood vessel:	n/a	n/a
28	ATF3	chr1:153505584-153507053	A549	lung:	n/a	n/a
29	GABPA	chr1:153505967-153506507	A549	lung:	n/a	n/a
30	SIN3AK20	chr1:153505416-153506776	A549	lung:	n/a	n/a
31	RCOR1	chr1:153505657-153506048	K562	blood:	n/a	n/a
32	POLR2A	chr1:153505437-153506814	MCF10A-Er-Src	breast:	n/a	n/a
33	RAD21	chr1:153505508-153506170	ECC-1	luminal epithelium:	n/a	chr1:153505773-153505792
34	YY1	chr1:153505471-153506062	H1-hESC	embryonic stem cell:	n/a	n/a
35	ELK1	chr1:153505691-153506950	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:153505198-153509437	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:153505162-153509201	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr1:153505225-153509006	ProgFib	skin:	n/a	n/a
39	RAD21	chr1:153505537-153506634	Hela-S3	cervix:	n/a	chr1:153505773-153505792
40	CHD2	chr1:153505437-153507025	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr1:153505749-153506689	A549	lung:	n/a	n/a
42	BRCA1	chr1:153505641-153506999	Hela-S3	cervix:	n/a	n/a
43	TCF7L2	chr1:153505258-153506096	PANC-1	pancreas:	n/a	n/a
44	SIN3AK20	chr1:153505636-153506671	A549	lung:	n/a	n/a
45	BCL3	chr1:153505257-153506994	A549	lung:	n/a	chr1:153505748-153505761 chr1:153506972-153506981 chr1:153506398-153506407 chr1:153506973-153506982
46	RAD21	chr1:153505308-153506983	HCT-116	colon:	n/a	chr1:153505323-153505336 chr1:153505773-153505792
47	SMARCB1	chr1:153505278-153507019	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr1:153505262-153506881	Gliobla	brain:	n/a	n/a
49	PBX3	chr1:153505178-153506863	A549	lung:	n/a	n/a
50	SIN3AK20	chr1:153505953-153506642	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153505804..153506639-chr19:11616185..11616790,2	Hela-S3	cervix:
2	chr1:153505949..153508623-chr1:153516119..153518362,2	K562	blood:
3	chr1:153505806..153506777-chr19:49468486..49469085,2	Hela-S3	cervix:
4	chr1:153505870..153508233-chr1:153598440..153600666,2	MCF-7	breast:
5	chr1:45987412..45988278-chr1:153505933..153506459,2	Hela-S3	cervix:
6	chr1:153505459..153506316-chr6:26199169..26200064,2	Hela-S3	cervix:
7	chr1:153505342..153508148-chr1:153641864..153643367,2	MCF-7	breast:
8	chr1:153505821..153506701-chr2:10266882..10267479,2	Hela-S3	cervix:
9	chr1:153505924..153506825-chr15:65596692..65597194,2	Hela-S3	cervix:
10	chr1:153505791..153506308-chr12:46122874..46123709,2	Hela-S3	cervix:
11	chr1:153504382..153507280-chr1:153522086..153523762,2	K562	blood:
12	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
13	chr1:153504329..153507150-chr1:153606463..153608211,3	MCF-7	breast:
14	chr1:153505866..153506777-chr14:75745220..75746209,2	Hela-S3	cervix:
15	chr1:153504925..153506891-chr1:153507588..153509186,2	K562	blood:
16	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
17	chr1:153505831..153506827-chr15:59041415..59041985,2	Hela-S3	cervix:
18	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
19	chr1:153505312..153506366-chr1:153540363..153541887,16	K562	blood:
20	chr1:153505791..153506334-chr17:73150204..73150802,2	Hela-S3	cervix:
21	chr1:153506024..153506652-chr14:24657445..24658442,2	Hela-S3	cervix:
22	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
23	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:
24	chr1:153505889..153508485-chr1:153582874..153585873,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238279	TF binding region
ENSG00000267477	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000189159	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000189079	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000137845	Chromatin interaction
ENSG00000161914	Chromatin interaction
ENSG00000087086	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000272030	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11488667	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11973	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835357	1.00[EUR][1000 genomes]
rs16835362	1.00[EUR][1000 genomes]
rs16835371	1.00[EUR][1000 genomes]
rs16835373	1.00[EUR][1000 genomes]
rs16835375	1.00[EUR][1000 genomes]
rs16835379	1.00[EUR][1000 genomes]
rs16835389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835413	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16835417	1.00[EUR][1000 genomes]
rs2104500	1.00[EUR][1000 genomes]
rs2230870	1.00[EUR][1000 genomes]
rs28373144	1.00[EUR][1000 genomes]
rs28407716	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28442251	1.00[EUR][1000 genomes]
rs28451322	1.00[EUR][1000 genomes]
rs28456342	1.00[EUR][1000 genomes]
rs28485860	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28510499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28578863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28587171	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28605603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28634320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28645589	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28648662	1.00[EUR][1000 genomes]
rs28690872	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28694652	1.00[EUR][1000 genomes]
rs28709866	1.00[EUR][1000 genomes]
rs28784102	1.00[EUR][1000 genomes]
rs3014827	1.00[EUR][1000 genomes]
rs3856025	1.00[EUR][1000 genomes]
rs56140059	1.00[EUR][1000 genomes]
rs56255753	1.00[EUR][1000 genomes]
rs56401460	1.00[EUR][1000 genomes]
rs58529054	1.00[EUR][1000 genomes]
rs59209384	1.00[EUR][1000 genomes]
rs59617976	1.00[EUR][1000 genomes]
rs60219287	1.00[EUR][1000 genomes]
rs60460123	1.00[EUR][1000 genomes]
rs61038462	1.00[EUR][1000 genomes]
rs61131911	1.00[EUR][1000 genomes]
rs61148582	1.00[EUR][1000 genomes]
rs73009954	1.00[EUR][1000 genomes]
rs73011738	1.00[EUR][1000 genomes]
rs73020460	1.00[EUR][1000 genomes]
rs73020461	1.00[EUR][1000 genomes]
rs73020464	1.00[EUR][1000 genomes]
rs73020467	1.00[EUR][1000 genomes]
rs73020468	1.00[EUR][1000 genomes]
rs73020471	1.00[EUR][1000 genomes]
rs73020473	1.00[EUR][1000 genomes]
rs73020474	1.00[EUR][1000 genomes]
rs73020478	1.00[EUR][1000 genomes]
rs73020479	1.00[EUR][1000 genomes]
rs73020496	1.00[EUR][1000 genomes]
rs73020497	1.00[EUR][1000 genomes]
rs73024502	1.00[EUR][1000 genomes]
rs73026308	1.00[EUR][1000 genomes]
rs730347	1.00[EUR][1000 genomes]
rs74115477	1.00[EUR][1000 genomes]
rs74115478	1.00[EUR][1000 genomes]
rs74115489	1.00[EUR][1000 genomes]
rs746425	1.00[EUR][1000 genomes]
rs7518794	1.00[EUR][1000 genomes]
rs7528738	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7543851	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153503400-153507200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:153503800-153507400	Enhancers	Small Intestine	intestine
3	chr1:153504000-153506400	Enhancers	Primary T cells from cord blood	blood
4	chr1:153504000-153507600	Enhancers	Fetal Thymus	thymus
5	chr1:153504200-153506600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr1:153504200-153507600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:153504400-153506800	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:153504400-153507000	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:153504600-153506200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr1:153504600-153506200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr1:153504600-153506400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr1:153504800-153506400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr1:153504800-153506600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:153504800-153507200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr1:153504800-153507200	Enhancers	Spleen	Spleen
16	chr1:153504800-153507800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:153504800-153507800	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr1:153504800-153508000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:153505000-153506400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr1:153505000-153506400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:153505000-153506600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:153505000-153506800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:153505000-153507000	Flanking Active TSS	Hela-S3	cervix
24	chr1:153505000-153507400	Enhancers	Liver	Liver
25	chr1:153505200-153506200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:153505200-153506200	Enhancers	Lung	lung
27	chr1:153505200-153506200	Flanking Active TSS	HSMM	muscle
28	chr1:153505200-153506200	Flanking Active TSS	NHDF-Ad	bronchial
29	chr1:153505200-153506400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:153505200-153506400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr1:153505200-153506600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:153505200-153506600	Flanking Active TSS	HepG2	liver
33	chr1:153505400-153506200	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr1:153505400-153506400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr1:153505400-153506400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:153505400-153506400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr1:153505400-153506400	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr1:153505400-153506600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:153505400-153506600	Flanking Active TSS	Fetal Muscle Trunk	muscle
40	chr1:153505400-153506600	Flanking Active TSS	K562	blood
41	chr1:153505400-153506800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr1:153505400-153506800	Flanking Active TSS	Stomach Mucosa	stomach
43	chr1:153505400-153507400	Enhancers	Pancreas	Pancrea
44	chr1:153505400-153507600	Enhancers	Fetal Lung	lung
45	chr1:153505400-153507600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr1:153505400-153507800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:153505400-153507800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr1:153505400-153507800	Flanking Active TSS	HUVEC	blood vessel
49	chr1:153505400-153508000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr1:153505400-153508000	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links