Variant report

Variant	rs28730510
Chromosome Location	chr6:30170057-30170058
allele	C/G
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	chr6:30164724..30168214-chr6:30169655..30171651,4	MCF-7	breast:
5	chr6:30164021..30166889-chr6:30166891..30170637,4	MCF-7	breast:
6	chr6:30168287..30170293-chr6:30179032..30181257,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234127	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12175655	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12660499	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17188113	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2074477	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2187980	0.82[EUR][1000 genomes]
rs2239531	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284167	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284171	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517602	0.89[ASN][1000 genomes]
rs41272587	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41272591	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4282437	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56307380	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62407543	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9348838	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9366754	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9368624	0.80[ASN][1000 genomes]
rs9378189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9378221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380156	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9391677	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9391802	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9405046	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28730510	HCG18	Cis_1M	lymphoblastoid	RTeQTL
rs28730510	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	chr6:30152000-30170600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:30152000-30172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:30156800-30174600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:30157000-30171800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:30158200-30173600	Weak transcription	Psoas Muscle	Psoas
10	chr6:30158400-30179600	Weak transcription	Fetal Brain Male	brain
11	chr6:30162600-30170600	Strong transcription	Dnd41	blood
12	chr6:30162800-30170600	Strong transcription	Fetal Thymus	thymus
13	chr6:30163800-30170600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:30167000-30173000	Weak transcription	Brain Germinal Matrix	brain
15	chr6:30167000-30178000	Weak transcription	Fetal Brain Female	brain
16	chr6:30167800-30170400	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr6:30168000-30170400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:30168000-30170400	Genic enhancers	HepG2	liver
19	chr6:30168200-30170400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr6:30168200-30171200	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr6:30168400-30170400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
22	chr6:30168400-30170600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
23	chr6:30168400-30174000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:30168600-30170400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr6:30168600-30171200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:30168600-30171600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:30168600-30171800	Weak transcription	Lung	lung
28	chr6:30168600-30172800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr6:30168600-30174000	Weak transcription	NH-A	brain
30	chr6:30168600-30174000	Weak transcription	NHLF	lung
31	chr6:30168800-30170200	Enhancers	Primary hematopoietic stem cells	blood
32	chr6:30168800-30170400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:30168800-30170400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:30168800-30170400	Enhancers	Spleen	Spleen
35	chr6:30168800-30170600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:30168800-30170800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr6:30168800-30170800	Enhancers	Duodenum Mucosa	Duodenum
38	chr6:30168800-30171400	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:30168800-30171600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:30168800-30171600	Weak transcription	Brain Substantia Nigra	brain
41	chr6:30168800-30171800	Weak transcription	Brain Angular Gyrus	brain
42	chr6:30168800-30173400	Weak transcription	Gastric	stomach
43	chr6:30168800-30174800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr6:30168800-30179800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr6:30169000-30170200	Enhancers	Primary B cells from cord blood	blood
46	chr6:30169000-30170400	Enhancers	Fetal Intestine Small	intestine
47	chr6:30169000-30171400	Weak transcription	HMEC	breast
48	chr6:30169000-30171600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:30169000-30171600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:30169000-30171800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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