Variant report

Variant	rs539170104
Chromosome Location	chr6:149639412-149639413
allele	A/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	HCFC1	chr6:149638010-149639454	Hela-S3	cervix:	n/a	n/a
2	RCOR1	chr6:149639378-149639421	Hela-S3	cervix:	n/a	n/a
3	E2F4	chr6:149637957-149639599	K562	blood:	n/a	chr6:149638871-149638880 chr6:149638628-149638638 chr6:149639539-149639548 chr6:149638865-149638875 chr6:149638663-149638672 chr6:149639539-149639551 chr6:149638117-149638127
4	POLR2A	chr6:149637920-149639978	GM18951	blood:	n/a	n/a
5	MAZ	chr6:149637125-149639723	IMR90	lung:	n/a	chr6:149639590-149639599 chr6:149639537-149639547
6	ELF1	chr6:149638799-149639428	K562	blood:	n/a	chr6:149639164-149639173
7	JUND	chr6:149637951-149640130	K562	blood:	n/a	chr6:149639590-149639597 chr6:149639589-149639599 chr6:149638290-149638299 chr6:149639408-149639417 chr6:149639590-149639598 chr6:149639591-149639602 chr6:149639590-149639598
8	MAZ	chr6:149637726-149640212	K562	blood:	n/a	chr6:149639590-149639599 chr6:149639537-149639547
9	ZNF143	chr6:149639165-149640192	GM12878	blood:	n/a	chr6:149639408-149639426 chr6:149639202-149639220
10	POLR2A	chr6:149637921-149639452	K562	blood:	n/a	n/a
11	REST	chr6:149637719-149640159	H1-neurons	neurons:	n/a	chr6:149639441-149639454 chr6:149639160-149639167 chr6:149639437-149639457 chr6:149638120-149638133 chr6:149639437-149639457 chr6:149639158-149639167
12	TAF1	chr6:149639024-149639423	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:149637876-149640263	GM18505	blood:	n/a	n/a
14	ZMIZ1	chr6:149639182-149639483	K562	blood:	n/a	n/a
15	POLR2A	chr6:149637900-149639424	HL-60	blood:	n/a	n/a
16	POLR2A	chr6:149637728-149640345	GM12878	blood:	n/a	n/a
17	ZBTB7A	chr6:149637938-149639911	K562	blood:	n/a	n/a
18	CREB1	chr6:149637892-149639789	HepG2	liver:	n/a	n/a
19	STAT1	chr6:149639154-149639493	GM12878	blood:	n/a	chr6:149639410-149639422 chr6:149639413-149639425 chr6:149639458-149639470 chr6:149639290-149639298 chr6:149639303-149639315
20	POLR2A	chr6:149637945-149639985	GM15510	blood:	n/a	n/a
21	YY1	chr6:149637905-149639542	GM12892	blood:	n/a	chr6:149639156-149639170 chr6:149638898-149638909 chr6:149639363-149639374 chr6:149638667-149638677 chr6:149638126-149638140 chr6:149638862-149638876 chr6:149638868-149638882 chr6:149638667-149638689 chr6:149638663-149638672
22	ZBTB7A	chr6:149639401-149639570	HepG2	liver:	n/a	n/a
23	ATF2	chr6:149639222-149640982	GM12878	blood:	n/a	n/a
24	SIN3AK20	chr6:149637944-149639482	MCF-7	breast:	n/a	n/a
25	EP300	chr6:149638213-149639475	ECC-1	luminal epithelium:	n/a	chr6:149638288-149638302 chr6:149638862-149638878 chr6:149638241-149638248
26	YY1	chr6:149639381-149639551	K562	blood:	n/a	chr6:149639539-149639548 chr6:149639540-149639551
27	ZBTB7A	chr6:149637846-149639791	ECC-1	luminal epithelium:	n/a	n/a
28	ZBTB7A	chr6:149639087-149639723	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr6:149637775-149640831	GM12892	blood:	n/a	n/a
30	NFIC	chr6:149639135-149641240	GM12878	blood:	n/a	n/a
31	CHD2	chr6:149637953-149639871	Hela-S3	cervix:	n/a	chr6:149639412-149639422 chr6:149638577-149638587 chr6:149638334-149638344
32	POLR2A	chr6:149638191-149639431	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr6:149637929-149639564	GM12878	blood:	n/a	n/a
34	ZBTB7A	chr6:149638738-149639915	K562	blood:	n/a	n/a
35	RUNX3	chr6:149639382-149640487	GM12878	blood:	n/a	n/a
36	MAZ	chr6:149638272-149639654	HepG2	liver:	n/a	chr6:149639590-149639599 chr6:149639537-149639547
37	MAX	chr6:149638912-149639479	MCF-7	breast:	n/a	n/a
38	POLR2A	chr6:149637905-149639518	H1-neurons	neurons:	n/a	n/a
39	SIN3AK20	chr6:149639408-149639546	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:149638984-149639480	GM12891	blood:	n/a	n/a
41	CHD2	chr6:149638025-149639755	HepG2	liver:	n/a	chr6:149639412-149639422 chr6:149638577-149638587 chr6:149638334-149638344
42	TBL1XR1	chr6:149639174-149640585	GM12878	blood:	n/a	n/a
43	HMGN3	chr6:149637956-149639810	K562	blood:	n/a	chr6:149639591-149639600
44	BHLHE40	chr6:149639174-149639612	GM12878	blood:	n/a	n/a
45	MAZ	chr6:149637726-149640418	GM12878	blood:	n/a	chr6:149639590-149639599 chr6:149639537-149639547
46	CHD2	chr6:149638180-149639535	H1-hESC	embryonic stem cell:	n/a	chr6:149639412-149639422 chr6:149638577-149638587 chr6:149638334-149638344
47	PAX5	chr6:149639160-149639543	GM12892	blood:	n/a	n/a
48	SIN3A	chr6:149639001-149640277	H1-hESC	embryonic stem cell:	n/a	chr6:149639007-149639018 chr6:149639236-149639247 chr6:149639444-149639457
49	ZEB1	chr6:149639325-149640104	GM12878	blood:	n/a	n/a
50	MYC	chr6:149639161-149639618	NB4	blood:	n/a	chr6:149639590-149639599 chr6:149639537-149639547

No.	Distal block	Cell Line	Cell type
1	chr6:149349779..149353985-chr6:149637379..149639962,5	MCF-7	breast:
2	chr6:149538892..149540721-chr6:149638148..149641111,2	MCF-7	breast:
3	chr6:149638315..149640262-chr6:149865472..149868393,2	K562	blood:
4	chr6:149636797..149639661-chr6:149663144..149666590,3	K562	blood:
5	chr6:149351823..149355344-chr6:149638842..149641991,4	MCF-7	breast:
6	chr6:149625453..149629470-chr6:149636058..149640474,5	MCF-7	breast:

Variant related genes	Relation type
TAB2	TF binding region
ENSG00000055208	Chromatin interaction
ENSG00000131013	Chromatin interaction
ENSG00000216265	Chromatin interaction
ENSG00000228408	Chromatin interaction
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1015360	chr6:149609804-149649982	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3377797	chr6:149637284-149640632	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
5	esv3365966	chr6:149637634-149640707	Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
6	esv3389424	chr6:149638059-149640257	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149637200-149639800	Active TSS	K562	blood
2	chr6:149637200-149640000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:149637200-149640200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:149637200-149640200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:149637200-149640400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:149637200-149640400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:149637200-149640800	Active TSS	A549	lung
8	chr6:149637200-149641000	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr6:149637400-149639600	Active TSS	Fetal Muscle Leg	muscle
10	chr6:149637400-149639600	Active TSS	Psoas Muscle	Psoas
11	chr6:149637400-149639800	Active TSS	Thymus	Thymus
12	chr6:149637400-149640200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:149637400-149640400	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr6:149637400-149640400	Active TSS	Right Ventricle	heart
15	chr6:149637400-149640400	Active TSS	Hela-S3	cervix
16	chr6:149637400-149640600	Active TSS	NHDF-Ad	bronchial
17	chr6:149637400-149640800	Active TSS	H1 Cell Line	embryonic stem cell
18	chr6:149637400-149640800	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr6:149637400-149640800	Active TSS	Brain Cingulate Gyrus	brain
20	chr6:149637400-149640800	Active TSS	Fetal Stomach	stomach
21	chr6:149637400-149641000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:149637400-149641200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr6:149637400-149641200	Active TSS	Brain Angular Gyrus	brain
24	chr6:149637400-149641200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:149637400-149641200	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr6:149637400-149641200	Active TSS	Stomach Smooth Muscle	stomach
27	chr6:149637400-149641200	Active TSS	HSMMtube	muscle
28	chr6:149637400-149641200	Active TSS	NH-A	brain
29	chr6:149637400-149641600	Active TSS	Brain Substantia Nigra	brain
30	chr6:149637400-149642000	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr6:149637400-149642600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:149637600-149639600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:149637600-149639600	Active TSS	Fetal Lung	lung
34	chr6:149637600-149639800	Active TSS	Duodenum Mucosa	Duodenum
35	chr6:149637600-149640200	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr6:149637600-149640200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:149637600-149640200	Active TSS	Brain Germinal Matrix	brain
38	chr6:149637600-149640200	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr6:149637600-149640400	Active TSS	H9 Cell Line	embryonic stem cell
40	chr6:149637600-149640400	Active TSS	Fetal Intestine Small	intestine
41	chr6:149637600-149640400	Active TSS	Fetal Muscle Trunk	muscle
42	chr6:149637600-149640600	Active TSS	Colonic Mucosa	Colon
43	chr6:149637600-149640800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:149637600-149640800	Active TSS	Brain Hippocampus Middle	brain
45	chr6:149637600-149640800	Active TSS	Colon Smooth Muscle	Colon
46	chr6:149637600-149640800	Active TSS	Ovary	ovary
47	chr6:149637600-149640800	Active TSS	Rectal Smooth Muscle	rectum
48	chr6:149637600-149640800	Active TSS	HSMM	muscle
49	chr6:149637600-149641000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:149637600-149641000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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