Variant report

Variant	rs210163
Chromosome Location	chr6:33561164-33561165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr6:33559961-33561426	GM12878	blood:	n/a	n/a
2	ZBTB7A	chr6:33560438-33561443	ECC-1	luminal epithelium:	n/a	n/a
3	ZBTB7A	chr6:33560395-33561493	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr6:33560971-33561433	GM12891	blood:	n/a	n/a
5	ESR1	chr6:33560816-33561248	ECC-1	luminal epithelium:	n/a	n/a
6	PAX5	chr6:33560129-33561311	GM12878	blood:	n/a	chr6:33561019-33561038 chr6:33560403-33560422
7	POLR2A	chr6:33561068-33561190	GM12878	blood:	n/a	n/a
8	CEBPB	chr6:33561096-33561164	H1-hESC	embryonic stem cell:	n/a	n/a
9	EP300	chr6:33560968-33561215	GM12878	blood:	n/a	chr6:33561174-33561190
10	PML	chr6:33559934-33561467	GM12878	blood:	n/a	n/a
11	CHD1	chr6:33561097-33561295	GM12878	blood:	n/a	n/a
12	STAT5A	chr6:33559941-33561548	GM12878	blood:	n/a	n/a
13	GABPA	chr6:33560917-33561301	H1-hESC	embryonic stem cell:	n/a	n/a
14	RELA	chr6:33560219-33561454	GM15510	blood:	n/a	n/a
15	POLR2A	chr6:33560932-33561364	ECC-1	luminal epithelium:	n/a	n/a
16	ELK1	chr6:33560978-33561202	GM12878	blood:	n/a	n/a
17	EBF1	chr6:33560721-33561302	GM12878	blood:	n/a	n/a
18	NFIC	chr6:33560447-33561563	ECC-1	luminal epithelium:	n/a	n/a
19	ELF1	chr6:33560137-33561408	GM12878	blood:	n/a	chr6:33561180-33561192
20	BACH1	chr6:33560763-33561165	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZNF143	chr6:33560837-33561348	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:33560866-33561328	GM12878	blood:	n/a	n/a
23	MAZ	chr6:33560239-33561242	GM12878	blood:	n/a	n/a
24	BCLAF1	chr6:33560764-33561395	GM12878	blood:	n/a	chr6:33561177-33561186
25	EGR1	chr6:33560688-33561267	ECC-1	luminal epithelium:	n/a	chr6:33561182-33561192
26	PAX5	chr6:33560078-33561324	GM12892	blood:	n/a	chr6:33561019-33561038 chr6:33560403-33560422
27	ZEB1	chr6:33560807-33561313	GM12878	blood:	n/a	n/a
28	PAX5	chr6:33560044-33561443	GM12878	blood:	n/a	chr6:33561019-33561038 chr6:33560403-33560422
29	POLR2A	chr6:33560782-33561500	GM12892	blood:	n/a	n/a
30	EP300	chr6:33560861-33561240	GM12878	blood:	n/a	chr6:33561174-33561190
31	POLR2A	chr6:33560862-33561359	GM19193	blood:	n/a	n/a
32	PAX5	chr6:33560823-33561228	GM12878	blood:	n/a	chr6:33561019-33561038
33	RCOR1	chr6:33560930-33561226	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:33560786-33561391	GM12878	blood:	n/a	n/a
35	MAX	chr6:33560882-33561297	H1-hESC	embryonic stem cell:	n/a	n/a
36	MXI1	chr6:33560996-33561218	GM12878	blood:	n/a	n/a
37	EP300	chr6:33560598-33561429	ECC-1	luminal epithelium:	n/a	chr6:33561174-33561190
38	NRF1	chr6:33560898-33561298	GM12878	blood:	n/a	n/a
39	ESR1	chr6:33560825-33561179	ECC-1	luminal epithelium:	n/a	n/a
40	TCF12	chr6:33560196-33561521	ECC-1	luminal epithelium:	n/a	n/a
41	RAD21	chr6:33560790-33561343	ECC-1	luminal epithelium:	n/a	n/a
42	PAX5	chr6:33560929-33561284	GM12891	blood:	n/a	chr6:33561019-33561038
43	SP1	chr6:33560764-33561294	GM12878	blood:	n/a	n/a
44	RUNX3	chr6:33560001-33561329	GM12878	blood:	n/a	n/a
45	PAX5	chr6:33560719-33561324	GM12878	blood:	n/a	chr6:33561019-33561038
46	TEAD4	chr6:33560348-33561458	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr6:33560742-33561372	GM12892	blood:	n/a	n/a
48	EP300	chr6:33560163-33561554	ECC-1	luminal epithelium:	n/a	chr6:33561174-33561190
49	POLR2A	chr6:33560409-33561372	GM12892	blood:	n/a	n/a
50	SMC3	chr6:33561127-33561187	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33555432..33562879-chr6:33670455..33680174,12	K562	blood:

Variant related genes	Relation type
LINC00336	TF binding region
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs210125	1.00[JPT][hapmap]
rs386906	0.81[EUR][1000 genomes]
rs420361	0.83[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs420628	0.83[EUR][1000 genomes]
rs422652	1.00[JPT][hapmap]
rs422907	0.81[EUR][1000 genomes]
rs430655	0.83[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs210163	ITPR3	cis	lymphoblastoid	seeQTL
rs210163	FKBP5	cis	cerebellum	SCAN
rs210163	C6orf125	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33555800-33561400	Enhancers	Spleen	Spleen
2	chr6:33556600-33561400	Enhancers	Lung	lung
3	chr6:33557000-33561400	Enhancers	HMEC	breast
4	chr6:33557600-33561200	Enhancers	Primary B cells from cord blood	blood
5	chr6:33558600-33567200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:33559000-33567200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:33559200-33561200	Weak transcription	Fetal Kidney	kidney
8	chr6:33559400-33562600	Weak transcription	A549	lung
9	chr6:33559400-33563000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:33559400-33567200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:33559600-33563000	Weak transcription	Hela-S3	cervix
12	chr6:33559600-33569800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:33559800-33562600	Weak transcription	HepG2	liver
14	chr6:33560000-33561400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:33560200-33561200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:33560200-33561600	Flanking Active TSS	GM12878-XiMat	blood
17	chr6:33560200-33561600	Enhancers	NHLF	lung
18	chr6:33560400-33561400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:33560400-33561400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr6:33560400-33561400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr6:33560400-33561400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr6:33560400-33561400	Active TSS	Brain Anterior Caudate	brain
23	chr6:33560400-33561400	Bivalent Enhancer	Fetal Brain Male	brain
24	chr6:33560400-33561400	Enhancers	Gastric	stomach
25	chr6:33560400-33561400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr6:33560400-33561600	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr6:33560400-33561600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr6:33560400-33561600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr6:33560600-33561200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr6:33560600-33561200	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr6:33560600-33561200	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr6:33560600-33561200	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr6:33560600-33561200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:33560600-33561200	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr6:33560600-33561200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:33560600-33561200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:33560600-33561200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:33560600-33561200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr6:33560600-33561400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:33560600-33561400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:33560600-33561400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:33560600-33561400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr6:33560600-33561400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:33560600-33561400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:33560600-33561400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:33560600-33561400	Active TSS	Brain Angular Gyrus	brain
47	chr6:33560600-33561400	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr6:33560600-33561400	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr6:33560600-33561400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr6:33560600-33561400	Bivalent Enhancer	Fetal Muscle Leg	muscle

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