Variant report

Variant	rs2517613
Chromosome Location	chr6:30165662-30165663
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30027674..30030498-chr6:30165364..30166955,2	MCF-7	breast:
2	chr6:30164991..30167307-chr6:30168742..30170547,2	K562	blood:
3	chr6:30164021..30166889-chr6:30166891..30170637,4	MCF-7	breast:
4	chr6:30164724..30168214-chr6:30169655..30171651,4	MCF-7	breast:
5	chr6:30161796..30164276-chr6:30165247..30166786,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204623	Chromatin interaction
ENSG00000066379	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2188100	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517612	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2517618	0.95[EUR][1000 genomes]
rs2523715	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2523719	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2523720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2844770	0.83[EUR][1000 genomes]
rs2844771	0.83[EUR][1000 genomes]
rs2844772	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2844773	0.83[EUR][1000 genomes]
rs2844785	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3129706	0.81[EUR][1000 genomes]
rs3129835	0.81[EUR][1000 genomes]
rs3129836	0.81[EUR][1000 genomes]
rs885913	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs885916	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs929157	0.89[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2517613	HLA-C	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	chr6:30150600-30179200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:30151800-30170400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:30152000-30166400	Strong transcription	Liver	Liver
6	chr6:30152000-30168000	Strong transcription	Fetal Intestine Large	intestine
7	chr6:30152000-30168200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr6:30152000-30168200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:30152000-30168200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:30152000-30169000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:30152000-30170600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:30152000-30172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:30152200-30167800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr6:30152200-30167800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr6:30152200-30168000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr6:30152200-30168200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:30152200-30168200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr6:30152200-30168600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:30152200-30169000	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:30152400-30167200	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr6:30152400-30168800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr6:30152400-30169000	Strong transcription	Adipose Nuclei	Adipose
23	chr6:30152600-30166000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:30153200-30169800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:30156800-30174600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:30157000-30171800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:30157600-30166600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:30158200-30173600	Weak transcription	Psoas Muscle	Psoas
29	chr6:30158400-30179600	Weak transcription	Fetal Brain Male	brain
30	chr6:30159000-30166800	Weak transcription	A549	lung
31	chr6:30161200-30167200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:30161200-30168400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr6:30161400-30168800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:30161400-30169200	Strong transcription	Placenta	Placenta
35	chr6:30161600-30168400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:30161600-30168800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr6:30161800-30166000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:30161800-30167200	Strong transcription	Brain Anterior Caudate	brain
39	chr6:30161800-30169000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:30162000-30167000	Strong transcription	Fetal Brain Female	brain
41	chr6:30162000-30169000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:30162000-30169000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:30162200-30168200	Strong transcription	Fetal Intestine Small	intestine
44	chr6:30162200-30169000	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:30162200-30169000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:30162400-30166200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:30162400-30167000	Strong transcription	Brain Germinal Matrix	brain
48	chr6:30162400-30167200	Strong transcription	Esophagus	oesophagus
49	chr6:30162400-30167200	Strong transcription	Pancreas	Pancrea
50	chr6:30162400-30167600	Strong transcription	HepG2	liver

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