Variant report

Variant	rs9386796
Chromosome Location	chr6:109618704-109618705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109616158..109619267-chr6:109664026..109668209,4	MCF-7	breast:
2	chr6:109604174..109607113-chr6:109618128..109619634,2	MCF-7	breast:
3	chr6:109618654..109620547-chr6:109621198..109623394,2	K562	blood:
4	chr6:109618104..109620663-chr6:109710406..109712166,2	MCF-7	breast:
5	chr6:109609293..109611431-chr6:109617491..109619119,2	MCF-7	breast:
6	chr6:109617424..109619147-chr6:109701372..109704187,2	MCF-7	breast:
7	chr6:109617393..109622773-chr6:109623823..109627648,7	K562	blood:
8	chr6:109505984..109508437-chr6:109617883..109620389,2	MCF-7	breast:
9	chr6:109617102..109620529-chr6:109701283..109704576,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000203799	Chromatin interaction
ENSG00000201023	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000233908	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1008084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1111863	0.88[CEU][hapmap]
rs1111865	0.88[CEU][hapmap]
rs1111866	0.88[CEU][hapmap]
rs11153165	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11153166	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11153167	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11153168	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11751953	0.94[ASN][1000 genomes]
rs11757567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961369	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966072	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12664455	0.90[ASN][1000 genomes]
rs13191948	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196219	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13196590	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs13200047	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13203155	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13219432	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219561	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341271	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521908	0.88[CEU][hapmap]
rs1546723	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351724	0.84[CEU][hapmap]
rs351725	0.84[CEU][hapmap]
rs351728	0.84[CEU][hapmap]
rs4548045	0.85[ASN][1000 genomes]
rs4601178	0.88[CEU][hapmap]
rs5005289	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55677234	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs59272337	0.92[ASN][1000 genomes]
rs6568569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568571	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919423	0.84[CEU][hapmap]
rs6924815	0.88[CEU][hapmap]
rs7748918	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772602	0.88[CEU][hapmap]
rs7773490	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs932223	0.84[CEU][hapmap]
rs9374076	0.94[ASN][1000 genomes]
rs9374080	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374081	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9386779	0.85[ASN][1000 genomes]
rs9386790	0.88[CEU][hapmap]
rs9386791	0.83[CEU][hapmap]
rs9386795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400265	0.94[ASN][1000 genomes]
rs9400269	0.88[CEU][hapmap]
rs9400271	0.88[CEU][hapmap]
rs9400272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480921	0.88[CEU][hapmap]
rs9480922	0.88[CEU][hapmap]
rs9480923	0.88[CEU][hapmap]
rs9480924	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487023	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9487033	0.88[CEU][hapmap]
rs9487034	0.88[CEU][hapmap]
rs9487036	0.83[CEU][hapmap]
rs9487048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487049	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9487051	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487052	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9386796	CD164	cis	parietal	SCAN
rs9386796	RAB40AL	trans	parietal	SCAN
rs9386796	GNPDA2	trans	cerebellum	SCAN
rs9386796	ATG5	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109613000-109619000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:109613200-109619000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:109613400-109620200	Weak transcription	Right Atrium	heart
4	chr6:109613600-109620600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:109614000-109619000	Weak transcription	Brain Substantia Nigra	brain
6	chr6:109614000-109622000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:109614200-109619000	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:109614400-109621000	Enhancers	Primary hematopoietic stem cells	blood
9	chr6:109614600-109619400	Enhancers	HepG2	liver
10	chr6:109614800-109624400	Enhancers	K562	blood
11	chr6:109615000-109619600	Enhancers	Fetal Intestine Large	intestine
12	chr6:109615200-109619400	Enhancers	Stomach Mucosa	stomach
13	chr6:109615200-109619800	Enhancers	Fetal Intestine Small	intestine
14	chr6:109615400-109624600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:109615600-109619000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:109615600-109619200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:109615600-109619200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:109615600-109619400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:109615600-109622200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:109615600-109622600	Weak transcription	Left Ventricle	heart
21	chr6:109615600-109622600	Weak transcription	Right Ventricle	heart
22	chr6:109615800-109619200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:109615800-109619200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:109615800-109620200	Weak transcription	Psoas Muscle	Psoas
25	chr6:109616200-109624400	Weak transcription	Hela-S3	cervix
26	chr6:109617200-109619600	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr6:109617200-109619600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:109617400-109619200	Enhancers	Stomach Smooth Muscle	stomach
29	chr6:109617400-109619400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:109617400-109620400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:109617600-109618800	Enhancers	Pancreas	Pancrea
32	chr6:109617600-109619400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr6:109617800-109618800	Enhancers	Duodenum Mucosa	Duodenum
34	chr6:109617800-109619200	Enhancers	Colonic Mucosa	Colon
35	chr6:109617800-109619400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr6:109617800-109621800	Enhancers	Fetal Lung	lung
37	chr6:109617800-109623200	Enhancers	Fetal Muscle Leg	muscle
38	chr6:109618000-109619600	Enhancers	Fetal Heart	heart
39	chr6:109618200-109618800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:109618200-109618800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:109618200-109618800	Enhancers	Gastric	stomach
42	chr6:109618200-109618800	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr6:109618200-109619200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:109618200-109619600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:109618200-109619800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr6:109618200-109621000	Enhancers	Fetal Muscle Trunk	muscle
47	chr6:109618200-109623400	Enhancers	Colon Smooth Muscle	Colon
48	chr6:109618400-109619000	Weak transcription	Brain Anterior Caudate	brain
49	chr6:109618400-109619200	Weak transcription	Fetal Thymus	thymus
50	chr6:109618400-109619400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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