Variant report

Variant	rs9468076
Chromosome Location	chr6:27338890-27338891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27337026..27338973-chr6:27341041..27343428,2	K562	blood:
2	chr6:27337172..27339325-chr6:27341568..27344928,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POM121L2-2	chr6:27337915-27339304	NONHSAT108367

Variant related genes	Relation type
ENSG00000124613	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1127574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1555040	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16867857	0.88[JPT][hapmap]
rs17688516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17739310	0.84[CHD][hapmap]
rs17739702	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17739727	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]
rs2064092	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs4145206	0.84[CHD][hapmap]
rs55923531	0.88[ASN][1000 genomes]
rs56388125	0.81[ASN][1000 genomes]
rs62622793	0.96[ASN][1000 genomes]
rs721600	0.92[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs72839482	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs764285	0.83[ASN][1000 genomes]
rs9348760	0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs9348761	0.94[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs9348762	0.84[EUR][1000 genomes]
rs9368502	0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs9379976	0.86[TSI][hapmap]
rs9379977	0.86[TSI][hapmap]
rs9379978	0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs9393805	0.86[TSI][hapmap]
rs9393807	0.87[YRI][hapmap]
rs9393808	0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs9461357	0.84[CHD][hapmap]
rs9461359	0.82[EUR][1000 genomes]
rs9461360	0.82[EUR][1000 genomes]
rs9461362	0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs9461363	0.86[ASN][1000 genomes]
rs9461366	0.83[ASN][1000 genomes]
rs9468047	0.82[YRI][hapmap]
rs9468067	0.84[CHD][hapmap]
rs9468068	0.85[YRI][hapmap]
rs9468069	0.82[EUR][1000 genomes]
rs9468149	0.90[CHD][hapmap];0.89[JPT][hapmap]
rs9468152	0.89[JPT][hapmap]
rs9468153	0.89[JPT][hapmap]
rs9468155	0.89[JPT][hapmap]
rs9468159	0.89[JPT][hapmap]

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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9468076	HIST1H2AL	cis	cerebellum	SCAN
rs9468076	BTN3A3	cis	cerebellum	SCAN
rs9468076	ZNF204P	cis	cerebellum	SCAN
rs9468076	ZNF391	cis	cerebellum	SCAN
rs9468076	HIST1H3H	cis	cerebellum	SCAN
rs9468076	HIST1H2AK	cis	parietal	SCAN
rs9468076	HIST1H2AC	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27326800-27342000	Weak transcription	Colonic Mucosa	Colon
2	chr6:27327000-27342000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:27327400-27341800	Weak transcription	Fetal Brain Male	brain
4	chr6:27327400-27341800	Weak transcription	Fetal Kidney	kidney
5	chr6:27327600-27342200	Weak transcription	Brain Substantia Nigra	brain
6	chr6:27328000-27342400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:27328200-27341800	Weak transcription	Adipose Nuclei	Adipose
8	chr6:27328200-27341800	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:27328200-27341800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:27328200-27342200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:27328400-27341800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:27329400-27341800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:27329800-27342000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:27330200-27341400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:27330600-27341800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:27330600-27341800	Weak transcription	Brain Anterior Caudate	brain
17	chr6:27331200-27341600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr6:27331200-27341800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:27331600-27342000	Weak transcription	Left Ventricle	heart
20	chr6:27334000-27341400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:27334000-27342200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:27336200-27341800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:27336200-27342000	Weak transcription	Gastric	stomach
24	chr6:27336400-27342000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:27336400-27342000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:27336400-27342000	Weak transcription	Right Atrium	heart
27	chr6:27336600-27341600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:27336600-27341600	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:27336600-27342000	Weak transcription	Pancreas	Pancrea
30	chr6:27336800-27341800	Weak transcription	Brain Angular Gyrus	brain
31	chr6:27336800-27341800	Weak transcription	Fetal Brain Female	brain
32	chr6:27336800-27341800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:27336800-27341800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:27336800-27342000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:27336800-27342000	Weak transcription	Fetal Intestine Large	intestine
36	chr6:27336800-27342000	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:27336800-27342000	Weak transcription	Right Ventricle	heart
38	chr6:27337000-27341800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:27337000-27341800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:27337000-27342000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:27337000-27342000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:27337000-27342000	Weak transcription	Aorta	Aorta
43	chr6:27337000-27342000	Weak transcription	Fetal Intestine Small	intestine
44	chr6:27337000-27342000	Weak transcription	Fetal Lung	lung
45	chr6:27337000-27342000	Weak transcription	Fetal Stomach	stomach
46	chr6:27337000-27342000	Weak transcription	Ovary	ovary
47	chr6:27337000-27342000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr6:27337000-27342200	Weak transcription	Esophagus	oesophagus
49	chr6:27337200-27341400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:27337200-27342000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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