Variant report

Variant	rs2523719
Chromosome Location	chr6:30168319-30168320
allele	A/C
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	chr6:30164021..30166889-chr6:30166891..30170637,4	MCF-7	breast:
3	chr6:30166782..30168897-chr6:30174962..30177557,2	K562	blood:
4	chr6:30156647..30159060-chr6:30167300..30168860,2	K562	blood:
5	chr6:30168287..30170293-chr6:30179032..30181257,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234127	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs2079171	1.00[ASN][1000 genomes]
rs2079172	1.00[ASN][1000 genomes]
rs2188100	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517612	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2517613	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2517615	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2517618	0.95[EUR][1000 genomes]
rs2523715	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2523720	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2844770	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2844771	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2844772	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2844773	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2844785	0.89[EUR][1000 genomes]
rs3129706	0.81[EUR][1000 genomes]
rs3129835	0.81[EUR][1000 genomes]
rs3129836	0.81[EUR][1000 genomes]
rs71561361	1.00[ASN][1000 genomes]
rs885913	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs885916	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs929157	0.89[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2523719	ZNF323	cis	parietal	SCAN
rs2523719	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs2523719	ZKSCAN3	cis	parietal	SCAN
rs2523719	ZNF192	cis	parietal	SCAN
rs2523719	BTN2A1	cis	parietal	SCAN

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	chr6:30152200-30168600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:30152200-30169000	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:30152400-30168800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr6:30152400-30169000	Strong transcription	Adipose Nuclei	Adipose
12	chr6:30153200-30169800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:30156800-30174600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:30157000-30171800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:30158200-30173600	Weak transcription	Psoas Muscle	Psoas
16	chr6:30158400-30179600	Weak transcription	Fetal Brain Male	brain
17	chr6:30161200-30168400	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:30161400-30168800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:30161400-30169200	Strong transcription	Placenta	Placenta
20	chr6:30161600-30168400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:30161600-30168800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:30161800-30169000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:30162000-30169000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:30162000-30169000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:30162200-30169000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:30162200-30169000	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:30162400-30168600	Strong transcription	Thymus	Thymus
28	chr6:30162400-30168800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr6:30162400-30168800	Strong transcription	Gastric	stomach
30	chr6:30162400-30169000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:30162400-30169000	Strong transcription	Colonic Mucosa	Colon
32	chr6:30162400-30169000	Strong transcription	Fetal Muscle Leg	muscle
33	chr6:30162400-30169000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr6:30162400-30169200	Strong transcription	Fetal Stomach	stomach
35	chr6:30162400-30169400	Strong transcription	Colon Smooth Muscle	Colon
36	chr6:30162600-30168800	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr6:30162600-30170600	Strong transcription	Dnd41	blood
38	chr6:30162800-30168400	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr6:30162800-30168400	Strong transcription	Spleen	Spleen
40	chr6:30162800-30168800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:30162800-30168800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:30162800-30168800	Strong transcription	Brain Hippocampus Middle	brain
43	chr6:30162800-30168800	Strong transcription	Left Ventricle	heart
44	chr6:30162800-30168800	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:30162800-30169000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:30162800-30169000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:30162800-30169000	Strong transcription	Fetal Lung	lung
48	chr6:30162800-30169400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:30162800-30169400	Strong transcription	Primary T cells from cord blood	blood
50	chr6:30162800-30169400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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