Variant report

Variant	rs11608416
Chromosome Location	chr12:121020933-121020934
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	CTCF	chr12:121020877-121021911	HCT-116	colon:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
2	CTCF	chr12:121020914-121022043	SK-N-SH	brain:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384
3	RAD21	chr12:121020884-121021974	SK-N-SH	brain:	n/a	chr12:121021368-121021387
4	CTCF	chr12:121020840-121020990	GM12868	blood:	n/a	n/a
5	CTCF	chr12:121020832-121022060	A549	lung:	n/a	chr12:121021367-121021385 chr12:121021372-121021382 chr12:121021369-121021390 chr12:121021368-121021384

No.	Distal block	Cell Line	Cell type
1	chr12:121018631..121021385-chr12:121124185..121125689,2	MCF-7	breast:
2	chr12:121015961..121017626-chr12:121019497..121021092,2	K562	blood:
3	chr12:121017632..121023235-chr12:121123750..121127979,5	K562	blood:
4	chr12:121019025..121020943-chr12:121076838..121078875,3	K562	blood:
5	chr12:120728472..120731126-chr12:121019042..121021642,2	K562	blood:
6	chr12:121020078..121022631-chr12:121125640..121127142,2	K562	blood:
7	chr12:121020907..121021484-chr12:121077869..121078415,2	MCF-7	breast:
8	chr12:121020899..121021841-chr12:121409286..121409915,3	K562	blood:
9	chr12:121020419..121023213-chr12:121085697..121088719,3	MCF-7	breast:
10	chr12:121020917..121021868-chr12:121533219..121533885,3	K562	blood:
11	chr12:121020875..121021804-chr12:121150905..121152345,4	K562	blood:
12	chr12:121019438..121021278-chr12:121153857..121156212,2	K562	blood:

Variant related genes	Relation type
POP5	TF binding region
ENSG00000167272	Chromatin interaction
ENSG00000110917	Chromatin interaction
ENSG00000256008	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000157782	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10789	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11065140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11065142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11612519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11613214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11614224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs16950293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16950305	0.86[JPT][hapmap]
rs2280168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3742049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3817301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4102203	1.00[CEU][hapmap]
rs7027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs719450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7296473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7964008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7973555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv973944	chr12:121017088-121027122	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121019600-121021200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:121019600-121021200	Weak transcription	Spleen	Spleen
3	chr12:121019600-121022000	Weak transcription	Lung	lung
4	chr12:121019600-121027200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:121019800-121021200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:121019800-121021200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:121019800-121021200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:121019800-121021200	Weak transcription	Esophagus	oesophagus
9	chr12:121019800-121021200	Weak transcription	Pancreas	Pancrea
10	chr12:121019800-121021400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:121019800-121021400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:121019800-121021400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:121019800-121021400	Weak transcription	Gastric	stomach
14	chr12:121019800-121021400	Weak transcription	Psoas Muscle	Psoas
15	chr12:121019800-121021400	Weak transcription	Stomach Mucosa	stomach
16	chr12:121019800-121022200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:121019800-121022200	Weak transcription	Aorta	Aorta
18	chr12:121019800-121022200	Weak transcription	Left Ventricle	heart
19	chr12:121019800-121022600	Weak transcription	Small Intestine	intestine
20	chr12:121020000-121021000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:121020000-121021000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:121020000-121021000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:121020000-121021000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:121020000-121021000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:121020000-121021000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:121020000-121021000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:121020000-121021000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:121020000-121021000	Weak transcription	Adipose Nuclei	Adipose
29	chr12:121020000-121021000	Weak transcription	Brain Angular Gyrus	brain
30	chr12:121020000-121021000	Weak transcription	Brain Anterior Caudate	brain
31	chr12:121020000-121021000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:121020000-121021000	Weak transcription	Brain Germinal Matrix	brain
33	chr12:121020000-121021000	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:121020000-121021000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:121020000-121021000	Weak transcription	Brain Substantia Nigra	brain
36	chr12:121020000-121021000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:121020000-121021000	Weak transcription	Fetal Heart	heart
38	chr12:121020000-121021000	Weak transcription	Fetal Intestine Small	intestine
39	chr12:121020000-121021000	Weak transcription	Fetal Kidney	kidney
40	chr12:121020000-121021000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr12:121020000-121021000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:121020000-121021200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:121020000-121021200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:121020000-121021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:121020000-121021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:121020000-121021200	Weak transcription	HSMM	muscle
47	chr12:121020000-121021200	Weak transcription	NH-A	brain
48	chr12:121020000-121021400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:121020000-121021400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:121020000-121021400	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links