Variant report

Variant	rs2237154
Chromosome Location	chr6:15400114-15400115
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	MYC	chr6:15399987-15401210	K562	blood:	n/a	chr6:15400130-15400140 chr6:15400060-15400070
2	MAX	chr6:15399944-15400821	Hela-S3	cervix:	n/a	chr6:15400130-15400140 chr6:15400060-15400070
3	REST	chr6:15399996-15400614	PFSK-1	brain:	n/a	chr6:15400252-15400262
4	MAX	chr6:15399904-15400716	SK-N-SH	brain:	n/a	chr6:15400130-15400140 chr6:15400060-15400070
5	USF2	chr6:15400110-15400228	Hela-S3	cervix:	n/a	n/a
6	EP300	chr6:15400048-15401084	SK-N-SH_RA	brain:	n/a	chr6:15400641-15400648 chr6:15400874-15400888 chr6:15400295-15400311
7	MYC	chr6:15399808-15400691	MCF10A-Er-Src	breast:	n/a	chr6:15400130-15400140 chr6:15400060-15400070
8	POLR2A	chr6:15400076-15400335	H1-hESC	embryonic stem cell:	n/a	n/a
9	REST	chr6:15400012-15400599	PFSK-1	brain:	n/a	chr6:15400252-15400262
10	CEBPD	chr6:15400108-15400602	K562	blood:	n/a	n/a
11	TCF12	chr6:15399950-15400929	SK-N-SH	brain:	n/a	n/a
12	MXI1	chr6:15399651-15401885	SK-N-SH	brain:	n/a	n/a
13	SIN3AK20	chr6:15400100-15400599	PFSK-1	brain:	n/a	n/a
14	NFIC	chr6:15400089-15400734	SK-N-SH	brain:	n/a	n/a
15	YY1	chr6:15399930-15400685	SK-N-SH_RA	brain:	n/a	chr6:15400455-15400466 chr6:15400426-15400437
16	GATA2	chr6:15400090-15401277	SH-SY5Y	brain:	n/a	chr6:15400621-15400632 chr6:15400876-15400886
17	EP300	chr6:15399976-15400836	SK-N-SH_RA	brain:	n/a	chr6:15400641-15400648 chr6:15400295-15400311 chr6:15399989-15400003
18	MAX	chr6:15399924-15400243	NB4	blood:	n/a	chr6:15400130-15400140 chr6:15400060-15400070
19	REST	chr6:15400081-15400591	K562	blood:	n/a	chr6:15400252-15400262
20	MAX	chr6:15399961-15400711	Hela-S3	cervix:	n/a	chr6:15400130-15400140 chr6:15400060-15400070
21	MAX	chr6:15399951-15400635	K562	blood:	n/a	chr6:15400130-15400140 chr6:15400060-15400070
22	ZNF263	chr6:15399983-15401389	HEK293-T-REx	kidney:	n/a	chr6:15401115-15401136
23	MYC	chr6:15399919-15400705	MCF10A-Er-Src	breast:	n/a	chr6:15400130-15400140 chr6:15400060-15400070
24	MAZ	chr6:15399883-15401362	IMR90	lung:	n/a	n/a
25	GATA3	chr6:15399986-15400716	MCF-7	breast:	n/a	chr6:15400621-15400632 chr6:15400023-15400033
26	PBX3	chr6:15400067-15400750	SK-N-SH	brain:	n/a	n/a
27	REST	chr6:15400077-15400364	Hela-S3	cervix:	n/a	chr6:15400252-15400262
28	MAX	chr6:15399841-15400726	K562	blood:	n/a	chr6:15400130-15400140 chr6:15400060-15400070
29	CBX3	chr6:15399893-15400643	K562	blood:	n/a	n/a
30	POLR2A	chr6:15399991-15400166	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr6:15399940-15400185	K562	blood:	n/a	n/a
32	TEAD4	chr6:15399999-15400682	SK-N-SH	brain:	n/a	n/a
33	TEAD4	chr6:15399946-15400695	K562	blood:	n/a	n/a
34	NFIC	chr6:15399975-15400908	SK-N-SH	brain:	n/a	n/a
35	MAX	chr6:15399921-15400576	K562	blood:	n/a	chr6:15400130-15400140 chr6:15400060-15400070
36	EP300	chr6:15399759-15401905	SK-N-SH	brain:	n/a	chr6:15400641-15400648 chr6:15400874-15400888 chr6:15401761-15401771 chr6:15401418-15401432 chr6:15400295-15400311 chr6:15399989-15400003
37	TCF12	chr6:15400005-15400804	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr6:15400049-15401349	PFSK-1	brain:	n/a	n/a
39	GATA3	chr6:15399982-15400829	SK-N-SH	brain:	n/a	chr6:15400621-15400632 chr6:15400023-15400033
40	GATA3	chr6:15400101-15400744	MCF-7	breast:	n/a	chr6:15400621-15400632
41	GATA3	chr6:15399977-15400842	SK-N-SH	brain:	n/a	chr6:15400621-15400632 chr6:15400023-15400033
42	RAD21	chr6:15400068-15400716	SK-N-SH_RA	brain:	n/a	chr6:15400300-15400314 chr6:15400681-15400691
43	MAX	chr6:15399960-15400144	H1-hESC	embryonic stem cell:	n/a	chr6:15400130-15400140 chr6:15400060-15400070
44	RFX5	chr6:15400106-15400708	Hela-S3	cervix:	n/a	n/a
45	MYC	chr6:15399937-15401166	K562	blood:	n/a	chr6:15400130-15400140 chr6:15400060-15400070

No.	Distal block	Cell Line	Cell type
1	chr6:15342546..15345320-chr6:15399209..15400740,2	K562	blood:
2	chr6:15368801..15370843-chr6:15397622..15400552,2	K562	blood:
3	chr6:15374975..15376583-chr6:15397138..15400134,2	MCF-7	breast:
4	chr1:28975037..28975540-chr6:15400031..15401028,2	Hela-S3	cervix:
5	chr6:15397861..15400160-chr6:15471488..15473543,2	K562	blood:
6	chr6:15211244..15213237-chr6:15398595..15400625,2	K562	blood:

Variant related genes	Relation type
JARID2	TF binding region
ENSG00000270103	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2237140	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2237155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2237156	0.91[CHB][hapmap]
rs2237158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2282825	0.81[JPT][hapmap]
rs2282826	0.82[JPT][hapmap]
rs2282827	0.82[JPT][hapmap]
rs2299053	0.91[CHB][hapmap]
rs2299054	0.91[CHB][hapmap]
rs2299056	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4109434	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.82[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9370813	0.91[CHB][hapmap]
rs9383054	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1019927	chr6:15351240-15419257	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv538145	chr6:15351240-15419257	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2237154	SIRT5	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15365000-15402800	Weak transcription	Dnd41	blood
2	chr6:15390800-15400200	Weak transcription	Aorta	Aorta
3	chr6:15391600-15400200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:15391800-15400200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:15392000-15400200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:15394600-15400200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:15396200-15400800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr6:15396200-15410200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr6:15396600-15400400	Enhancers	H9 Cell Line	embryonic stem cell
10	chr6:15396800-15401200	Enhancers	Small Intestine	intestine
11	chr6:15397400-15405600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:15397600-15400400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:15397600-15400400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr6:15397600-15401800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:15397600-15405800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:15398000-15400200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:15398000-15400400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:15398000-15406000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr6:15398400-15400200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:15398400-15400800	Enhancers	Primary B cells from peripheral blood	blood
21	chr6:15398400-15405600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr6:15398600-15400200	Enhancers	Brain Anterior Caudate	brain
23	chr6:15398600-15400800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:15398600-15401400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:15398600-15401600	Enhancers	Primary B cells from cord blood	blood
26	chr6:15398600-15405800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr6:15398600-15406600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr6:15398800-15400200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:15398800-15400200	Enhancers	Colon Smooth Muscle	Colon
30	chr6:15398800-15400200	Enhancers	Psoas Muscle	Psoas
31	chr6:15398800-15400400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr6:15398800-15400800	Enhancers	Primary T cells from cord blood	blood
33	chr6:15398800-15401400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:15398800-15401600	Enhancers	Fetal Thymus	thymus
35	chr6:15399000-15400200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:15399000-15400200	Enhancers	Brain Substantia Nigra	brain
37	chr6:15399000-15400200	Enhancers	Right Atrium	heart
38	chr6:15399000-15400200	Enhancers	Right Ventricle	heart
39	chr6:15399000-15400400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr6:15399000-15400400	Enhancers	Left Ventricle	heart
41	chr6:15399000-15400800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr6:15399000-15402600	Enhancers	NHEK	skin
43	chr6:15399000-15404200	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr6:15399000-15410600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:15399200-15400200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:15399200-15400200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:15399200-15400200	Enhancers	Fetal Stomach	stomach
48	chr6:15399200-15400200	Enhancers	Spleen	Spleen
49	chr6:15399200-15400200	Enhancers	NH-A	brain
50	chr6:15399200-15400400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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