Variant report

Variant	rs9382254
Chromosome Location	chr6:53776584-53776585
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53773618..53775142-chr6:53776237..53778157,2	K562	blood:
2	chr6:53775665..53777635-chr6:53782933..53785644,2	MCF-7	breast:
3	chr6:53774348..53776830-chr6:53777789..53780459,2	MCF-7	breast:
4	chr6:53658683..53661137-chr6:53774256..53778054,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000271218	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10755766	0.80[AMR][1000 genomes]
rs1076701	0.94[CEU][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1076702	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10948775	0.80[AMR][1000 genomes]
rs2073020	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2294789	0.92[EUR][1000 genomes]
rs2294790	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2294791	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3777661	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4265034	0.82[ASN][1000 genomes]
rs4314499	0.82[AMR][1000 genomes]
rs4624872	0.85[CHB][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs6903399	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6906921	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs6907027	0.85[CHB][hapmap]
rs6921605	0.83[MEX][hapmap]
rs7751036	0.81[CHB][hapmap]
rs9296722	0.82[ASN][1000 genomes]
rs9349685	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357776	0.94[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9357778	0.82[EUR][1000 genomes]
rs9370233	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9370241	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9370244	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9370246	0.82[EUR][1000 genomes]
rs9382232	0.80[AMR][1000 genomes]
rs9382233	0.80[AMR][1000 genomes]
rs9382238	0.85[EUR][1000 genomes]
rs9382241	0.85[EUR][1000 genomes]
rs9382243	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9382244	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382246	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382248	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382252	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382253	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382256	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382257	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9395876	0.80[AMR][1000 genomes]
rs9395878	1.00[CEU][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs9395881	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9395884	0.80[ASN][1000 genomes]
rs9395887	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9382254	LRRC1	cis	lymphoblastoid	seeQTL
rs9382254	HMGCLL1	cis	parietal	SCAN
rs9382254	ZNF451	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53752800-53782000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:53754800-53779800	Weak transcription	NHLF	lung
3	chr6:53755000-53779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:53756000-53781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
6	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
7	chr6:53759400-53786400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
10	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
11	chr6:53760600-53778800	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:53761000-53782000	Weak transcription	Fetal Kidney	kidney
14	chr6:53761000-53782800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:53761000-53785400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:53761400-53787400	Weak transcription	HMEC	breast
17	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart
19	chr6:53761800-53777000	Strong transcription	Fetal Thymus	thymus
20	chr6:53761800-53786800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:53762000-53791200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
23	chr6:53762200-53786800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:53764400-53784600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:53768600-53785000	Weak transcription	Primary B cells from cord blood	blood
26	chr6:53768800-53778600	Weak transcription	Aorta	Aorta
27	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:53769000-53785400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:53769200-53777000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:53769200-53778600	Weak transcription	Esophagus	oesophagus
31	chr6:53769200-53790400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:53769400-53777600	Weak transcription	Small Intestine	intestine
33	chr6:53769600-53785200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:53769800-53779000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:53769800-53784400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:53769800-53784400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:53770000-53778600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:53770000-53778600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:53770000-53781800	Weak transcription	HSMM	muscle
40	chr6:53770000-53782000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:53770000-53795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:53770400-53778800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr6:53770600-53787400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:53770800-53778600	Weak transcription	Fetal Stomach	stomach
45	chr6:53771200-53778600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr6:53771200-53778600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:53771200-53778600	Weak transcription	Thymus	Thymus
48	chr6:53771200-53785000	Weak transcription	Left Ventricle	heart
49	chr6:53771400-53778400	Weak transcription	HepG2	liver
50	chr6:53771600-53778000	Enhancers	Brain Inferior Temporal Lobe	brain

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