Variant report

Variant	rs2517617
Chromosome Location	chr6:30161536-30161537
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	chr6:30028645..30030852-chr6:30160087..30161687,2	K562	blood:

Variant related genes	Relation type
ENSG00000066379	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11158	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1573296	0.91[EUR][1000 genomes]
rs1970	0.91[EUR][1000 genomes]
rs2023473	0.85[EUR][1000 genomes]
rs2106072	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2157678	0.91[EUR][1000 genomes]
rs2517609	1.00[EUR][1000 genomes]
rs2517622	0.93[EUR][1000 genomes]
rs2523712	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2523729	0.93[EUR][1000 genomes]
rs2523978	0.85[EUR][1000 genomes]
rs2844777	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2844789	0.88[EUR][1000 genomes]
rs3094054	0.88[EUR][1000 genomes]
rs3094056	0.88[EUR][1000 genomes]
rs3094057	0.88[EUR][1000 genomes]
rs3094058	0.88[EUR][1000 genomes]
rs3094064	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3094066	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3094067	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3094069	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3094078	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3094620	0.88[EUR][1000 genomes]
rs3094624	0.88[EUR][1000 genomes]
rs3094625	0.88[EUR][1000 genomes]
rs3094628	0.88[EUR][1000 genomes]
rs3129815	0.88[EUR][1000 genomes]
rs3129830	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3130350	0.88[EUR][1000 genomes]
rs3130351	0.88[EUR][1000 genomes]
rs3130352	0.88[EUR][1000 genomes]
rs3130353	0.88[EUR][1000 genomes]
rs3130355	0.90[EUR][1000 genomes]
rs3130364	0.88[EUR][1000 genomes]
rs3130377	0.88[EUR][1000 genomes]
rs3130380	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3130399	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3132647	0.88[EUR][1000 genomes]
rs3132648	0.88[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2517617	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs2517617	BTN3A2	Cis_chr	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	chr6:30150200-30163400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:30150600-30179200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:30151800-30170400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:30152000-30166400	Strong transcription	Liver	Liver
7	chr6:30152000-30168000	Strong transcription	Fetal Intestine Large	intestine
8	chr6:30152000-30168200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr6:30152000-30168200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:30152000-30168200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:30152000-30169000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:30152000-30170600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:30152000-30172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:30152200-30167800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr6:30152200-30167800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr6:30152200-30168000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr6:30152200-30168200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:30152200-30168200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr6:30152200-30168600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:30152200-30169000	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:30152400-30167200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:30152400-30168800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr6:30152400-30169000	Strong transcription	Adipose Nuclei	Adipose
24	chr6:30152600-30166000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:30152800-30163000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:30153200-30169800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:30156000-30161800	Strong transcription	GM12878-XiMat	blood
28	chr6:30156600-30164600	Weak transcription	HSMM	muscle
29	chr6:30156800-30162800	Weak transcription	NHDF-Ad	bronchial
30	chr6:30156800-30174600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:30157000-30171800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr6:30157200-30162800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:30157200-30164600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:30157600-30166600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:30158200-30163000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:30158200-30163200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:30158200-30164200	Weak transcription	HUVEC	blood vessel
38	chr6:30158200-30173600	Weak transcription	Psoas Muscle	Psoas
39	chr6:30158400-30162800	Weak transcription	Brain Substantia Nigra	brain
40	chr6:30158400-30163200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr6:30158400-30179600	Weak transcription	Fetal Brain Male	brain
42	chr6:30158600-30162800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:30158600-30164600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:30158800-30161600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:30158800-30162800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr6:30158800-30162800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:30158800-30164200	Weak transcription	HMEC	breast
48	chr6:30158800-30164800	Weak transcription	Stomach Mucosa	stomach
49	chr6:30158800-30165400	Weak transcription	Fetal Kidney	kidney
50	chr6:30159000-30163000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links