Variant report

Variant	rs2033226
Chromosome Location	chr6:39182401-39182402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39162734..39164328-chr6:39181033..39182674,2	K562	blood:
2	chr6:39181537..39183525-chr6:39264253..39266272,2	K562	blood:
3	chr6:39177427..39182769-chr6:39182785..39188256,10	K562	blood:
4	chr6:39167002..39169864-chr6:39179599..39183167,3	K562	blood:
5	chr6:39173383..39177261-chr6:39181456..39183734,4	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10807202	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947786	0.84[CHB][hapmap]
rs10947787	0.90[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947788	0.92[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10947789	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12190363	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12200013	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12202900	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12207689	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711585	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714223	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714224	1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs55818834	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6918122	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72851851	0.86[EUR][1000 genomes];0.99[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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2033226	TDRG1	cis	cerebellum	SCAN
rs2033226	PRICKLE4	cis	parietal	SCAN
rs2033226	LHFPL5	cis	parietal	SCAN
rs2033226	PI16	cis	cerebellum	SCAN
rs2033226	TREM2	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39150600-39193800	Genic enhancers	Fetal Intestine Small	intestine
2	chr6:39156800-39193400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:39163800-39192800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:39169400-39193600	Enhancers	Liver	Liver
5	chr6:39174200-39195000	Enhancers	Stomach Mucosa	stomach
6	chr6:39177600-39182800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:39177600-39186400	Weak transcription	Primary T cells from cord blood	blood
8	chr6:39177800-39183400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:39178000-39183400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:39178000-39193400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:39178200-39182800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr6:39178200-39183000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr6:39178200-39184400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:39178200-39185000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:39178200-39185000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:39178200-39185200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:39178200-39186600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:39178400-39182600	Weak transcription	Hela-S3	cervix
19	chr6:39178400-39185000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:39178400-39185200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:39178600-39193200	Weak transcription	Thymus	Thymus
22	chr6:39178800-39184800	Genic enhancers	Fetal Intestine Large	intestine
23	chr6:39179000-39186200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:39179000-39186800	Genic enhancers	Fetal Thymus	thymus
25	chr6:39179200-39183000	Weak transcription	GM12878-XiMat	blood
26	chr6:39179200-39183200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:39179200-39184400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:39179200-39186200	Weak transcription	Small Intestine	intestine
29	chr6:39180000-39184000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:39180000-39184600	Strong transcription	Fetal Stomach	stomach
31	chr6:39180200-39184200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:39180200-39184600	Genic enhancers	Duodenum Mucosa	Duodenum
33	chr6:39180400-39183600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:39181000-39182800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:39181000-39184600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr6:39181200-39183400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:39181200-39183600	Enhancers	Esophagus	oesophagus
38	chr6:39181400-39182600	Weak transcription	Spleen	Spleen
39	chr6:39181400-39183000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:39181400-39183400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr6:39181600-39182800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:39181600-39185000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr6:39181800-39182800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
44	chr6:39181800-39189400	Genic enhancers	K562	blood
45	chr6:39182000-39182800	Genic enhancers	Rectal Mucosa Donor 31	rectum
46	chr6:39182000-39183000	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:39182000-39183000	Genic enhancers	Colonic Mucosa	Colon
48	chr6:39182000-39183000	Strong transcription	Placenta	Placenta
49	chr6:39182000-39183000	Genic enhancers	Gastric	stomach
50	chr6:39182000-39183200	Enhancers	Right Atrium	heart

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