Variant report

Variant	rs16986964
Chromosome Location	chr22:29409068-29409069
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29405475..29407089-chr22:29407777..29410693,2	MCF-7	breast:
2	chr22:29382490..29384756-chr22:29408678..29411279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183579	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16986970	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16987068	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56752813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57111962	1.00[AMR][1000 genomes]
rs57724605	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59264876	1.00[AMR][1000 genomes]
rs60213855	1.00[AMR][1000 genomes]
rs6519768	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881171	1.00[AMR][1000 genomes]
rs73881179	1.00[AMR][1000 genomes]
rs73881184	1.00[AMR][1000 genomes]
rs73881191	1.00[AMR][1000 genomes]
rs73881193	1.00[AMR][1000 genomes]
rs73882412	1.00[AMR][1000 genomes]
rs73882417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73882419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73882420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73882421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73882423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73882432	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73882446	1.00[AMR][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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29400600-29412000	Weak transcription	A549	lung
2	chr22:29400600-29425400	Weak transcription	NHEK	skin
3	chr22:29401200-29413400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr22:29401400-29414800	Weak transcription	Esophagus	oesophagus
5	chr22:29401400-29419200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr22:29401400-29425000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr22:29401800-29426200	Weak transcription	Colon Smooth Muscle	Colon
8	chr22:29402600-29412000	Weak transcription	Pancreas	Pancrea
9	chr22:29402800-29411400	Genic enhancers	HepG2	liver
10	chr22:29404800-29411000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr22:29405200-29418000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr22:29405400-29410200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr22:29405400-29410400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr22:29405400-29424600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr22:29406400-29409200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr22:29406400-29410800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr22:29406600-29410800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr22:29407000-29409600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr22:29407000-29409600	Enhancers	Fetal Lung	lung
20	chr22:29407000-29410600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr22:29407000-29411000	Enhancers	Fetal Intestine Large	intestine
22	chr22:29407000-29411000	Genic enhancers	Fetal Intestine Small	intestine
23	chr22:29407200-29409200	Enhancers	Fetal Muscle Leg	muscle
24	chr22:29407200-29409200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr22:29407200-29409600	Enhancers	Small Intestine	intestine
26	chr22:29407200-29410400	Enhancers	Psoas Muscle	Psoas
27	chr22:29407200-29411000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr22:29407400-29409400	Enhancers	Aorta	Aorta
29	chr22:29407400-29410400	Weak transcription	Lung	lung
30	chr22:29407800-29409600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:29407800-29409800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr22:29407800-29410000	Weak transcription	Brain Substantia Nigra	brain
33	chr22:29407800-29410600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr22:29407800-29413400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr22:29408000-29409600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr22:29408000-29410000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr22:29408000-29410200	Weak transcription	Right Ventricle	heart
38	chr22:29408200-29409200	Enhancers	Brain Cingulate Gyrus	brain
39	chr22:29408200-29409400	Enhancers	Brain Germinal Matrix	brain
40	chr22:29408200-29410400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr22:29408200-29411600	Enhancers	Brain Anterior Caudate	brain
42	chr22:29408200-29412000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr22:29408200-29419400	Weak transcription	Fetal Stomach	stomach
44	chr22:29408200-29419400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr22:29408200-29422600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr22:29408400-29409600	Enhancers	Duodenum Mucosa	Duodenum
47	chr22:29408400-29410000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr22:29408400-29410000	Weak transcription	Fetal Heart	heart
49	chr22:29408400-29410000	Weak transcription	Fetal Kidney	kidney
50	chr22:29408400-29410200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links