Variant report

Variant	rs9461006
Chromosome Location	chr6:24433483-24433484
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	chr6:24431522..24434175-chr6:24447084..24450027,2	MCF-7	breast:
2	chr6:24432825..24434367-chr6:24500694..24503119,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1042303	0.87[YRI][hapmap]
rs1054862	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1054868	0.93[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1133526	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11695	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16889240	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16889242	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16889253	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16901722	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs17306130	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1772256	0.83[LWK][hapmap]
rs2273606	0.93[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2298059	0.93[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2298060	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28564434	0.84[AFR][1000 genomes]
rs28706811	0.85[AFR][1000 genomes]
rs3469	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747771	0.93[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747772	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3818936	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3827641	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41271775	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41271777	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41271781	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45448393	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45478094	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45482500	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45574139	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs45590133	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56148439	0.88[AFR][1000 genomes]
rs7751846	0.94[LWK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs7752186	0.94[LWK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs7752603	0.91[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs7757601	0.91[YRI][hapmap]
rs7768124	0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs7772115	0.94[LWK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs7772540	0.94[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs9461007	0.92[AFR][1000 genomes]
rs9461008	0.88[AFR][1000 genomes]
rs9461009	0.89[AFR][1000 genomes]
rs9467136	0.91[YRI][hapmap]
rs9467142	0.93[AFR][1000 genomes]
rs9467143	0.94[AFR][1000 genomes]
rs9467144	0.85[AFR][1000 genomes]
rs9467145	0.87[AFR][1000 genomes]
rs9467146	0.85[AFR][1000 genomes]
rs9467147	0.85[AFR][1000 genomes]
rs9467150	0.85[AFR][1000 genomes]
rs9467151	0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs9467152	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs9467153	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs9467154	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs9467159	0.85[AFR][1000 genomes]
rs9467163	0.81[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9461006	HIST1H2AC	cis	cerebellum	SCAN
rs9461006	MRS2	cis	cerebellum	SCAN
rs9461006	ZNF184	cis	parietal	SCAN
rs9461006	HIST1H2BG	cis	parietal	SCAN
rs9461006	GPLD1	cis	Esophagus Muscularis	GTEx
rs9461006	HIST1H4A	cis	cerebellum	SCAN
rs9461006	MRS2L	Cis_1M	lymphoblastoid	RTeQTL
rs9461006	TDP2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24404600-24437400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:24417400-24451800	Strong transcription	Liver	Liver
3	chr6:24421200-24448800	Weak transcription	Gastric	stomach
4	chr6:24421200-24459600	Weak transcription	Spleen	Spleen
5	chr6:24421400-24434000	Weak transcription	Fetal Brain Male	brain
6	chr6:24422400-24437400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:24423400-24433600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:24423400-24437200	Weak transcription	Pancreas	Pancrea
9	chr6:24423400-24439400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:24423600-24437200	Weak transcription	Right Ventricle	heart
11	chr6:24424000-24456600	Weak transcription	Ovary	ovary
12	chr6:24424400-24445800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:24425400-24437200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:24425400-24439600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:24426000-24438800	Weak transcription	Brain Substantia Nigra	brain
16	chr6:24426200-24446000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:24426400-24441600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:24426400-24446000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:24426600-24438800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:24427200-24433800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:24427400-24435000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:24427600-24433800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:24427600-24436600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:24427600-24437600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:24427600-24439200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:24427600-24439400	Weak transcription	Fetal Thymus	thymus
27	chr6:24427600-24440000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:24427600-24440000	Weak transcription	Dnd41	blood
29	chr6:24427600-24441800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr6:24427600-24445600	Weak transcription	Fetal Brain Female	brain
31	chr6:24427600-24456800	Weak transcription	Lung	lung
32	chr6:24427800-24435800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:24427800-24467000	Weak transcription	Brain Germinal Matrix	brain
34	chr6:24428200-24438000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:24428200-24449400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:24428800-24445000	Weak transcription	Psoas Muscle	Psoas
37	chr6:24429000-24447800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:24429000-24494200	Weak transcription	Primary B cells from cord blood	blood
39	chr6:24429200-24455600	Weak transcription	Brain Angular Gyrus	brain
40	chr6:24429400-24437000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:24429400-24438600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:24429400-24445000	Weak transcription	Brain Anterior Caudate	brain
43	chr6:24429400-24483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:24429600-24433600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr6:24429600-24436600	Weak transcription	Fetal Muscle Leg	muscle
46	chr6:24429600-24437400	Weak transcription	Aorta	Aorta
47	chr6:24429600-24444800	Weak transcription	HepG2	liver
48	chr6:24429600-24455000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:24429800-24434600	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:24430000-24436600	Weak transcription	Thymus	Thymus

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