Variant report

Variant	rs9470233
Chromosome Location	chr6:36195048-36195049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36194675..36197496-chr6:36231763..36234212,2	K562	blood:
2	chr6:36163358..36168297-chr6:36191373..36197382,8	K562	blood:
3	chr6:36187527..36189506-chr6:36193052..36195234,2	MCF-7	breast:
4	chr6:36161641..36166728-chr6:36193210..36198515,8	K562	blood:
5	chr6:36187119..36188817-chr6:36194570..36197402,2	MCF-7	breast:
6	chr6:36194084..36196042-chr6:36196761..36199323,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000096070	Chromatin interaction
ENSG00000246982	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2239798	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2859129	0.80[CEU][hapmap]
rs2859131	0.80[CEU][hapmap]
rs4236049	0.83[ASW][hapmap];0.87[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs4395718	0.87[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs4713940	0.87[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs4713941	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs59200830	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462161	0.87[CEU][hapmap];0.93[JPT][hapmap]
rs9462162	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9462164	1.00[ASW][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs9462165	0.94[ASW][hapmap];0.93[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9470222	0.87[CEU][hapmap];0.93[JPT][hapmap]
rs9470226	0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap]
rs9470229	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470230	0.94[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];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9470234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9470233	C6orf222	cis	parietal	SCAN
rs9470233	MAPK13	cis	cerebellum	SCAN
rs9470233	ANKS1A	cis	cerebellum	SCAN
rs9470233	MAPK14	cis	cerebellum	SCAN
rs9470233	CLPS	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36164400-36203000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:36166600-36200200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:36166800-36201800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:36167000-36201800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:36167200-36201400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:36167400-36201600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:36167600-36199800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:36167600-36201200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:36167800-36201400	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr6:36168000-36196800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:36168000-36200400	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr6:36168000-36201400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:36168200-36195400	Strong transcription	Placenta	Placenta
14	chr6:36169400-36201800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:36170000-36201800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:36172200-36202000	Strong transcription	Thymus	Thymus
17	chr6:36172600-36201400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr6:36172600-36201600	Strong transcription	Liver	Liver
19	chr6:36172600-36202000	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:36172800-36195200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:36172800-36195600	Strong transcription	Fetal Thymus	thymus
22	chr6:36173000-36201200	Strong transcription	Dnd41	blood
23	chr6:36173400-36202600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:36174000-36204600	Strong transcription	Primary T cells from cord blood	blood
25	chr6:36174200-36201800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr6:36174400-36201600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:36179400-36197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:36180400-36196200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:36183600-36199200	Genic enhancers	Fetal Intestine Small	intestine
30	chr6:36185800-36196600	Weak transcription	Fetal Brain Male	brain
31	chr6:36185800-36210600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:36186200-36202600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr6:36186400-36196800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:36187200-36195400	Weak transcription	Stomach Mucosa	stomach
35	chr6:36188400-36195600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:36188600-36195200	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:36188600-36195800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr6:36189000-36202600	Strong transcription	Fetal Muscle Leg	muscle
39	chr6:36189000-36204800	Strong transcription	Fetal Stomach	stomach
40	chr6:36189200-36201400	Strong transcription	Osteobl	bone
41	chr6:36189200-36202400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:36189400-36200200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr6:36189400-36201400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:36189400-36201400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:36189600-36200000	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr6:36189600-36200200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:36189600-36201200	Strong transcription	Fetal Lung	lung
48	chr6:36189600-36201400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:36189600-36201800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:36189600-36201800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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