Variant report

Variant	rs9996611
Chromosome Location	chr4:129780054-129780055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129772388..129774921-chr4:129778989..129781160,2	MCF-7	breast:
2	chr4:129731868..129734211-chr4:129779413..129782328,2	K562	blood:

Variant related genes	Relation type
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10006958	0.88[AFR][1000 genomes]
rs10008441	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10014385	1.00[AMR][1000 genomes]
rs10015538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10026447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028545	1.00[AMR][1000 genomes]
rs28430630	0.88[AFR][1000 genomes]
rs28434631	0.83[AFR][1000 genomes]
rs28583676	0.88[AFR][1000 genomes]
rs28707598	0.88[AFR][1000 genomes]
rs28823671	1.00[AMR][1000 genomes]
rs9307610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9991702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9994585	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1026938	chr4:129770961-129936205	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv870175	chr4:129771718-129937945	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1026772	chr4:129773881-129936205	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv461637	chr4:129774375-129924977	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv595397	chr4:129774375-129924977	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv461638	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv595398	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv1018994	chr4:129775612-129933968	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv4504	chr4:129777368-129803959	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv1034996	chr4:129777825-129905255	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv537249	chr4:129777825-129905255	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv1022446	chr4:129778025-129905116	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv537250	chr4:129778025-129905116	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv1030296	chr4:129778025-129920680	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
18	nsv537251	chr4:129778025-129920680	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
19	esv3427113	chr4:129778302-129782700	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129753600-129798600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:129753800-129795000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:129760400-129783400	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:129761600-129782000	Strong transcription	Fetal Intestine Small	intestine
5	chr4:129761600-129785000	Strong transcription	Thymus	Thymus
6	chr4:129762000-129782800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr4:129762400-129784200	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr4:129762800-129784200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr4:129763000-129783800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:129763000-129785800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:129763000-129787200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:129763200-129784000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:129763200-129784000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:129763400-129784200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:129763600-129780400	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr4:129763600-129786600	Strong transcription	Fetal Intestine Large	intestine
17	chr4:129763800-129780400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:129763800-129780400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr4:129763800-129783400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:129763800-129784000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr4:129763800-129784200	Strong transcription	Brain Germinal Matrix	brain
22	chr4:129764000-129784000	Strong transcription	Fetal Brain Female	brain
23	chr4:129766600-129780200	Strong transcription	Adipose Nuclei	Adipose
24	chr4:129766600-129780200	Strong transcription	Lung	lung
25	chr4:129766600-129783400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:129766600-129784200	Strong transcription	HepG2	liver
27	chr4:129767200-129784400	Strong transcription	Aorta	Aorta
28	chr4:129767400-129783800	Strong transcription	Brain Angular Gyrus	brain
29	chr4:129767400-129784000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:129767600-129780200	Strong transcription	Stomach Smooth Muscle	stomach
31	chr4:129767800-129784200	Strong transcription	Liver	Liver
32	chr4:129768000-129780400	Strong transcription	Gastric	stomach
33	chr4:129768000-129784000	Strong transcription	Brain Anterior Caudate	brain
34	chr4:129768600-129784000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:129768800-129780200	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:129768800-129784400	Weak transcription	Stomach Mucosa	stomach
37	chr4:129769200-129783600	Strong transcription	A549	lung
38	chr4:129769800-129784200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:129770600-129784000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:129772200-129780400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:129772600-129786000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr4:129773200-129794000	Strong transcription	K562	blood
43	chr4:129773400-129783800	Strong transcription	Brain Hippocampus Middle	brain
44	chr4:129774000-129788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr4:129775400-129782000	Strong transcription	NHEK	skin
46	chr4:129775400-129782600	Strong transcription	Fetal Thymus	thymus
47	chr4:129775800-129782600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:129775800-129782800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr4:129776000-129780400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:129776000-129780400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links