Variant report

Variant	rs2239531
Chromosome Location	chr6:30168829-30168830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30168209..30170458-chr6:30175226..30176879,2	MCF-7	breast:
2	chr6:30164991..30167307-chr6:30168742..30170547,2	K562	blood:
3	chr6:30168637..30170794-chr6:30170971..30172497,2	K562	blood:
4	chr6:30164021..30166889-chr6:30166891..30170637,4	MCF-7	breast:
5	chr6:30166782..30168897-chr6:30174962..30177557,2	K562	blood:
6	chr6:30156647..30159060-chr6:30167300..30168860,2	K562	blood:
7	chr6:30168287..30170293-chr6:30179032..30181257,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234127	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12175655	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12660499	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17188015	0.81[EUR][1000 genomes]
rs17188113	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2074477	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2187980	0.83[EUR][1000 genomes]
rs2284167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284171	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517602	0.89[ASN][1000 genomes]
rs28730510	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815081	0.81[EUR][1000 genomes]
rs41272587	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41272591	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4282437	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56307380	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62407543	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9348838	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9366754	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9368622	0.81[EUR][1000 genomes]
rs9368624	0.80[ASN][1000 genomes]
rs9378189	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9378221	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380156	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9391677	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9391802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9405046	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2239531	HCG18	Cis_1M	lymphoblastoid	RTeQTL
rs2239531	TRIM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30145000-30173800	Weak transcription	Right Atrium	heart
2	chr6:30148000-30173000	Weak transcription	Fetal Heart	heart
3	chr6:30150600-30179200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:30151800-30170400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:30152000-30169000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:30152000-30170600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:30152000-30172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:30152200-30169000	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:30152400-30169000	Strong transcription	Adipose Nuclei	Adipose
10	chr6:30153200-30169800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:30156800-30174600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:30157000-30171800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:30158200-30173600	Weak transcription	Psoas Muscle	Psoas
14	chr6:30158400-30179600	Weak transcription	Fetal Brain Male	brain
15	chr6:30161400-30169200	Strong transcription	Placenta	Placenta
16	chr6:30161800-30169000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:30162000-30169000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:30162000-30169000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:30162200-30169000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:30162200-30169000	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:30162400-30169000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:30162400-30169000	Strong transcription	Colonic Mucosa	Colon
23	chr6:30162400-30169000	Strong transcription	Fetal Muscle Leg	muscle
24	chr6:30162400-30169000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr6:30162400-30169200	Strong transcription	Fetal Stomach	stomach
26	chr6:30162400-30169400	Strong transcription	Colon Smooth Muscle	Colon
27	chr6:30162600-30170600	Strong transcription	Dnd41	blood
28	chr6:30162800-30169000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:30162800-30169000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:30162800-30169000	Strong transcription	Fetal Lung	lung
31	chr6:30162800-30169400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:30162800-30169400	Strong transcription	Primary T cells from cord blood	blood
33	chr6:30162800-30169400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:30162800-30170600	Strong transcription	Fetal Thymus	thymus
35	chr6:30163000-30169000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:30163400-30169200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:30163600-30169000	Strong transcription	Right Ventricle	heart
38	chr6:30163600-30169000	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:30163800-30169000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:30163800-30169000	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr6:30163800-30170600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:30164200-30169000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:30164400-30169000	Strong transcription	Hela-S3	cervix
44	chr6:30164600-30169000	Strong transcription	HSMM	muscle
45	chr6:30164600-30169200	Strong transcription	Osteobl	bone
46	chr6:30165400-30169000	Strong transcription	Fetal Kidney	kidney
47	chr6:30166200-30170000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr6:30166400-30169600	Weak transcription	Stomach Mucosa	stomach
49	chr6:30166600-30169000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:30166600-30169000	Strong transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links