Variant report

Variant	rs12939008
Chromosome Location	chr17:38599596-38599597
allele	C/G
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	MAX	chr17:38598612-38602497	A549	lung:	n/a	chr17:38599856-38599866
2	POLR2A	chr17:38599363-38600748	A549	lung:	n/a	n/a
3	E2F6	chr17:38599584-38600309	H1-hESC	embryonic stem cell:	n/a	chr17:38599728-38599737
4	BCL3	chr17:38598687-38599634	A549	lung:	n/a	chr17:38599413-38599426
5	POLR2A	chr17:38599559-38600771	A549	lung:	n/a	n/a
6	CTCFL	chr17:38599467-38599606	K562	blood:	n/a	n/a
7	CTCF	chr17:38599460-38599610	GM12868	blood:	n/a	n/a
8	CTCF	chr17:38599500-38599650	HMEC	breast:	n/a	n/a
9	POLR2A	chr17:38599592-38600150	HepG2	liver:	n/a	n/a
10	POLR2A	chr17:38599266-38599869	K562	blood:	n/a	n/a
11	E2F6	chr17:38598792-38600332	A549	lung:	n/a	chr17:38599127-38599139 chr17:38599728-38599737
12	E2F6	chr17:38599373-38600324	K562	blood:	n/a	chr17:38599728-38599737
13	CTCF	chr17:38599454-38599677	K562	blood:	n/a	n/a
14	POLR2A	chr17:38599286-38601272	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr17:38599127-38601091	A549	lung:	n/a	n/a
16	JUND	chr17:38599464-38600216	A549	lung:	n/a	chr17:38599725-38599734
17	POLR2A	chr17:38599081-38600304	NB4	blood:	n/a	n/a
18	POLR2A	chr17:38599331-38602347	IMR90	lung:	n/a	n/a
19	ZBTB7A	chr17:38599565-38599744	HepG2	liver:	n/a	n/a
20	POLR2A	chr17:38599391-38599862	K562	blood:	n/a	n/a
21	CTCF	chr17:38599500-38599650	HepG2	liver:	n/a	n/a
22	TAF1	chr17:38599220-38599927	A549	lung:	n/a	n/a
23	MAZ	chr17:38598638-38602479	IMR90	lung:	n/a	chr17:38599856-38599866
24	TAF1	chr17:38599338-38599789	K562	blood:	n/a	n/a
25	CTCF	chr17:38599560-38599710	GM12874	blood:	n/a	n/a
26	E2F6	chr17:38599418-38600204	K562	blood:	n/a	chr17:38599728-38599737
27	CTCF	chr17:38599512-38599606	GM10266	blood:	n/a	n/a
28	CTCF	chr17:38599520-38599670	HUVEC	blood vessel:	n/a	n/a
29	MYC	chr17:38599389-38600384	NB4	blood:	n/a	chr17:38599856-38599866
30	POLR2A	chr17:38599386-38602496	HUVEC	blood vessel:	n/a	n/a
31	REST	chr17:38598745-38599611	A549	lung:	n/a	chr17:38599288-38599297 chr17:38599043-38599056 chr17:38599270-38599280
32	POLR2A	chr17:38599346-38600157	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr17:38598990-38600252	K562	blood:	n/a	n/a
34	CTCF	chr17:38599573-38599617	H1-hESC	embryonic stem cell:	n/a	n/a
35	SMC3	chr17:38599162-38601066	SK-N-SH	brain:	n/a	chr17:38599730-38599740
36	CTCF	chr17:38598478-38602583	A549	lung:	n/a	n/a
37	POLR2A	chr17:38598937-38600627	MCF-7	breast:	n/a	n/a
38	SP1	chr17:38598759-38599889	A549	lung:	n/a	chr17:38599373-38599385 chr17:38599375-38599384 chr17:38599373-38599385 chr17:38599713-38599727 chr17:38599706-38599720 chr17:38599652-38599662 chr17:38599127-38599136 chr17:38599652-38599662
39	CTCF	chr17:38599468-38599622	Spleen_OC	spleen:	n/a	n/a
40	MAX	chr17:38599510-38600493	HepG2	liver:	n/a	chr17:38599856-38599866
41	POLR2A	chr17:38598935-38600621	PFSK-1	brain:	n/a	n/a
42	MAX	chr17:38598727-38600587	A549	lung:	n/a	chr17:38599856-38599866
43	E2F6	chr17:38599569-38600371	H1-hESC	embryonic stem cell:	n/a	chr17:38599728-38599737
44	POLR2A	chr17:38598691-38600986	MCF-7	breast:	n/a	n/a
45	TAF1	chr17:38599596-38599886	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr17:38599460-38599610	Caco-2	colon:	n/a	n/a
47	TBP	chr17:38599214-38600140	H1-hESC	embryonic stem cell:	n/a	n/a
48	HMGN3	chr17:38598981-38600351	K562	blood:	n/a	n/a
49	MAX	chr17:38599514-38600481	H1-hESC	embryonic stem cell:	n/a	chr17:38599856-38599866
50	CTCF	chr17:38599460-38599610	SAEC	small airway:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38461615..38484404-chr17:38597525..38608992,85	MCF-7	breast:
2	chr17:38516138..38520860-chr17:38599243..38602533,5	K562	blood:
3	chr17:38597471..38599668-chr17:38689776..38691457,2	K562	blood:
4	chr17:38571221..38576195-chr17:38597437..38603899,8	K562	blood:
5	chr17:38507026..38508719-chr17:38598987..38601879,2	K562	blood:
6	chr17:38555377..38556004-chr17:38599008..38599961,2	K562	blood:
7	chr17:38598881..38602329-chr17:38713858..38720847,8	MCF-7	breast:
8	chr17:38518063..38521220-chr17:38597683..38601473,5	MCF-7	breast:
9	chr17:38597908..38601053-chr17:38654458..38659532,5	MCF-7	breast:
10	chr17:38336165..38338939-chr17:38598006..38600043,2	MCF-7	breast:
11	chr17:38598261..38600683-chr9:136220142..136221734,2	MCF-7	breast:
12	chr17:38255561..38257319-chr17:38599585..38601482,2	K562	blood:
13	chr17:38572047..38583621-chr17:38597341..38605150,24	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240125	TF binding region
IGFBP4	TF binding region
ENSG00000126353	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000183153	Chromatin interaction
ENSG00000148290	Chromatin interaction
ENSG00000131747	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000126368	Chromatin interaction
ENSG00000131746	Chromatin interaction
ENSG00000266208	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv908223	chr17:38530799-38609187	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3442525	chr17:38598451-38601299	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	esv3384974	chr17:38598726-38601149	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38584600-38600200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:38598800-38599600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:38598800-38599600	Flanking Active TSS	Colonic Mucosa	Colon
4	chr17:38598800-38599600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr17:38598800-38599600	Flanking Active TSS	Dnd41	blood
6	chr17:38598800-38599800	Active TSS	Primary hematopoietic stem cells	blood
7	chr17:38598800-38600800	Active TSS	Brain Angular Gyrus	brain
8	chr17:38598800-38601400	Weak transcription	Hela-S3	cervix
9	chr17:38598800-38601800	Active TSS	H9 Cell Line	embryonic stem cell
10	chr17:38599000-38599600	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr17:38599000-38599600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr17:38599000-38599600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:38599000-38599600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr17:38599000-38599600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr17:38599000-38599600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr17:38599000-38599600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr17:38599000-38599600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
18	chr17:38599000-38599600	Flanking Active TSS	Fetal Brain Female	brain
19	chr17:38599000-38599600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
20	chr17:38599000-38599600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
21	chr17:38599000-38599600	Flanking Active TSS	Placenta	Placenta
22	chr17:38599000-38599800	Active TSS	Pancreas	Pancrea
23	chr17:38599000-38599800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
24	chr17:38599000-38600000	Enhancers	Primary B cells from cord blood	blood
25	chr17:38599000-38600000	Active TSS	Right Ventricle	heart
26	chr17:38599000-38600200	Bivalent/Poised TSS	Thymus	Thymus
27	chr17:38599000-38600400	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr17:38599000-38601200	Active TSS	Fetal Kidney	kidney
29	chr17:38599000-38601600	Active TSS	Esophagus	oesophagus
30	chr17:38599000-38602000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr17:38599000-38602200	Active TSS	Brain Anterior Caudate	brain
32	chr17:38599000-38602400	Active TSS	Psoas Muscle	Psoas
33	chr17:38599000-38602800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr17:38599000-38602800	Active TSS	Ovary	ovary
35	chr17:38599200-38599600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
36	chr17:38599200-38599600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
37	chr17:38599200-38599600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
38	chr17:38599200-38599600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:38599200-38599600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr17:38599200-38599600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr17:38599200-38599600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr17:38599200-38599600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr17:38599200-38599600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr17:38599200-38599600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
45	chr17:38599200-38599600	Flanking Active TSS	HMEC	breast
46	chr17:38599200-38599800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr17:38599200-38600200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:38599200-38600200	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr17:38599200-38600200	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr17:38599200-38600200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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