Variant report

Variant	rs2502642
Chromosome Location	chr6:144614132-144614133
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	chr6:144613353..144615831-chr6:144616673..144618969,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1322447	0.83[ASN][1000 genomes]
rs2017652	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2473130	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2473131	0.83[ASN][1000 genomes]
rs2473132	0.80[ASN][1000 genomes]
rs2473133	0.82[ASN][1000 genomes]
rs2473134	0.83[ASN][1000 genomes]
rs2473135	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2473136	0.98[EUR][1000 genomes]
rs2473137	0.98[EUR][1000 genomes]
rs2473138	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2473139	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2473140	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2473141	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2473142	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2473143	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2473144	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2473145	0.81[ASN][1000 genomes]
rs2473146	0.96[EUR][1000 genomes]
rs2473148	0.96[EUR][1000 genomes]
rs2473149	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2473150	0.95[EUR][1000 genomes]
rs2473151	0.92[EUR][1000 genomes]
rs2502628	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2502630	0.95[EUR][1000 genomes]
rs2502631	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2502635	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2502637	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2502638	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2502639	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2502643	0.98[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	nsv830831	chr6:144501371-144649509	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144608400-144626600	Weak transcription	Spleen	Spleen
2	chr6:144608600-144616600	Weak transcription	Pancreas	Pancrea
3	chr6:144608600-144616800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:144608600-144617200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:144608600-144617200	Weak transcription	Gastric	stomach
6	chr6:144608600-144617800	Weak transcription	Stomach Mucosa	stomach
7	chr6:144608600-144619400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:144608600-144626800	Weak transcription	Esophagus	oesophagus
9	chr6:144608600-144629800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:144608600-144631400	Weak transcription	Colonic Mucosa	Colon
11	chr6:144608800-144616800	Weak transcription	Fetal Intestine Large	intestine
12	chr6:144608800-144617600	Weak transcription	Right Atrium	heart
13	chr6:144609000-144616400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:144609000-144616800	Weak transcription	Aorta	Aorta
15	chr6:144609200-144614400	Weak transcription	NHEK	skin
16	chr6:144609200-144616000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:144609200-144616400	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:144609200-144616400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:144609200-144616600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:144609200-144616600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:144609200-144616600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:144609200-144616600	Weak transcription	Left Ventricle	heart
23	chr6:144609200-144616800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:144609200-144616800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:144609200-144616800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:144609200-144616800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:144609200-144616800	Weak transcription	Fetal Lung	lung
28	chr6:144609200-144616800	Weak transcription	Fetal Stomach	stomach
29	chr6:144609200-144617000	Weak transcription	Right Ventricle	heart
30	chr6:144609200-144617200	Weak transcription	Fetal Intestine Small	intestine
31	chr6:144609200-144617200	Weak transcription	Psoas Muscle	Psoas
32	chr6:144609200-144617800	Weak transcription	Brain Anterior Caudate	brain
33	chr6:144609200-144617800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:144609200-144618000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:144609200-144618000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:144609200-144618200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:144609200-144618600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr6:144609200-144623800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:144609200-144623800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:144609200-144626800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:144609200-144641600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr6:144609400-144614600	Weak transcription	NH-A	brain
43	chr6:144609400-144616400	Weak transcription	Fetal Kidney	kidney
44	chr6:144609400-144616400	Weak transcription	Dnd41	blood
45	chr6:144609400-144616800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:144609400-144616800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:144609400-144616800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr6:144609400-144617600	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:144609400-144617600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:144609600-144614800	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links