Variant report

Variant	rs236989
Chromosome Location	chr4:88013924-88013925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87927030..87929816-chr4:88013244..88015675,3	MCF-7	breast:
2	chr4:87854447..87858210-chr4:88013360..88015983,3	K562	blood:
3	chr4:88013784..88016288-chr4:88023619..88027731,5	MCF-7	breast:
4	chr4:87843821..87845327-chr4:88013319..88016028,2	MCF-7	breast:
5	chr4:87926137..87929773-chr4:88012891..88016296,3	K562	blood:
6	chr4:87854883..87857377-chr4:88013074..88015993,4	MCF-7	breast:
7	chr4:87855131..87857677-chr4:88011511..88016191,4	MCF-7	breast:
8	chr4:87843288..87844189-chr4:88013665..88015393,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10006308	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10010932	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021180	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021879	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028134	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489045	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012341	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012361	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189333	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236988	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236990	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904154	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342455	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57516814	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877982	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995808	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 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	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:87995400-88037800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:87995800-88023800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:87996800-88023600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:88000400-88020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:88001400-88025200	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:88001600-88014000	Weak transcription	Small Intestine	intestine
8	chr4:88001800-88025200	Weak transcription	Gastric	stomach
9	chr4:88003400-88028600	Weak transcription	HSMMtube	muscle
10	chr4:88004200-88019200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr4:88004400-88025200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:88005000-88017400	Strong transcription	Dnd41	blood
13	chr4:88005800-88014000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:88007600-88014400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:88007600-88018200	Weak transcription	Thymus	Thymus
16	chr4:88008600-88014000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:88008600-88014000	Weak transcription	Aorta	Aorta
18	chr4:88008800-88014000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:88008800-88014000	Weak transcription	NHLF	lung
20	chr4:88008800-88014200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:88008800-88015000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:88009000-88017800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:88009400-88017600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:88009800-88014000	Strong transcription	Placenta	Placenta
25	chr4:88010200-88014000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:88010200-88014000	Weak transcription	Ovary	ovary
27	chr4:88010200-88015000	Weak transcription	Esophagus	oesophagus
28	chr4:88010200-88018200	Weak transcription	Lung	lung
29	chr4:88010400-88014000	Weak transcription	Brain Substantia Nigra	brain
30	chr4:88010400-88014000	Weak transcription	Pancreas	Pancrea
31	chr4:88010400-88014000	Weak transcription	Spleen	Spleen
32	chr4:88010600-88014200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:88010600-88014800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:88010600-88015200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr4:88010600-88018400	Strong transcription	Fetal Thymus	thymus
36	chr4:88010800-88014000	Weak transcription	Right Ventricle	heart
37	chr4:88011400-88014000	Weak transcription	NHDF-Ad	bronchial
38	chr4:88011600-88014000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:88011600-88019000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:88011800-88014200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:88011800-88014200	Weak transcription	Fetal Kidney	kidney
42	chr4:88011800-88015600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:88011800-88022400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:88011800-88032800	Weak transcription	Colonic Mucosa	Colon
45	chr4:88012000-88015000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr4:88012000-88018000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:88012000-88021400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:88012200-88015200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr4:88012800-88014200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:88012800-88015400	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links