Variant report

Variant	rs200946
Chromosome Location	chr6:27834245-27834246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:226)
CpG islands
(count:0)
Chromatin interactive
region (count:38)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:226 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr6:27834115-27835485	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:27831639-27835944	MCF-7	breast:	n/a	n/a
3	NFIC	chr6:27832621-27835576	GM12878	blood:	n/a	n/a
4	YY1	chr6:27833725-27834864	H1-hESC	embryonic stem cell:	n/a	chr6:27834547-27834559
5	TAF7	chr6:27832651-27836396	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPD	chr6:27833466-27835530	K562	blood:	n/a	n/a
7	TAF1	chr6:27833784-27835580	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:27831681-27835663	MCF-7	breast:	n/a	n/a
9	JUND	chr6:27833370-27835526	SK-N-SH	brain:	n/a	chr6:27834282-27834291
10	STAT5A	chr6:27832583-27835747	GM12878	blood:	n/a	chr6:27835602-27835610
11	CREB1	chr6:27833361-27835634	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:27832618-27835481	GM12891	blood:	n/a	n/a
13	USF1	chr6:27833963-27834530	H1-hESC	embryonic stem cell:	n/a	n/a
14	ELF1	chr6:27833747-27835539	GM12878	blood:	n/a	n/a
15	YY1	chr6:27834077-27835531	GM12878	blood:	n/a	chr6:27834547-27834559 chr6:27835445-27835454
16	POLR2A	chr6:27832869-27835570	Gliobla	brain:	n/a	n/a
17	FOXM1	chr6:27832627-27835722	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:27832745-27835566	GM10847	blood:	n/a	n/a
19	BACH1	chr6:27834120-27834548	K562	blood:	n/a	n/a
20	POLR2A	chr6:27832732-27835534	HUVEC	blood vessel:	n/a	n/a
21	PML	chr6:27832883-27835592	MCF-7	breast:	n/a	n/a
22	POLR2A	chr6:27832669-27835567	MCF10A-Er-Src	breast:	n/a	n/a
23	RELA	chr6:27833925-27835514	GM18526	blood:	n/a	n/a
24	HEY1	chr6:27832629-27835529	K562	blood:	n/a	chr6:27832940-27832949 chr6:27832942-27832951
25	POLR2A	chr6:27832608-27835555	GM15510	blood:	n/a	n/a
26	MYC	chr6:27833855-27836057	NB4	blood:	n/a	n/a
27	POLR2A	chr6:27832654-27835691	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr6:27832719-27835560	GM12878	blood:	n/a	n/a
29	POLR2A	chr6:27834083-27835506	HepG2	liver:	n/a	n/a
30	TAL1	chr6:27833463-27834754	K562	blood:	n/a	n/a
31	POLR2A	chr6:27832846-27835535	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr6:27832605-27835544	GM12878	blood:	n/a	n/a
33	MAX	chr6:27833874-27834692	NB4	blood:	n/a	n/a
34	ATF2	chr6:27832684-27835681	H1-hESC	embryonic stem cell:	n/a	n/a
35	PAX5	chr6:27832656-27835467	GM12878	blood:	n/a	chr6:27833102-27833111
36	RELA	chr6:27832719-27835527	GM18951	blood:	n/a	n/a
37	NFIC	chr6:27833847-27835730	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr6:27832736-27835657	U87	brain:	n/a	n/a
39	POLR2A	chr6:27833935-27835515	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:27832620-27835499	GM12892	blood:	n/a	n/a
41	MAX	chr6:27833801-27834650	SK-N-SH	brain:	n/a	n/a
42	RXRA	chr6:27834161-27835043	GM12878	blood:	n/a	n/a
43	TCF12	chr6:27833698-27835699	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr6:27833878-27835543	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:27832537-27835575	GM12892	blood:	n/a	n/a
46	POLR2A	chr6:27833712-27835496	K562	blood:	n/a	n/a
47	GATA3	chr6:27833763-27835606	MCF-7	breast:	n/a	n/a
48	RELA	chr6:27832621-27835665	GM18505	blood:	n/a	n/a
49	NFYA	chr6:27834157-27834425	Hela-S3	cervix:	n/a	chr6:27834277-27834289 chr6:27834278-27834292 chr6:27834278-27834291 chr6:27834280-27834290 chr6:27834278-27834293 chr6:27834278-27834293
50	POLR2A	chr6:27832540-27835501	GM12878	blood:	n/a	n/a

No data

(count:38 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26054611..26058222-chr6:27833185..27835454,4	MCF-7	breast:
2	chr1:116915588..116917427-chr6:27834235..27836471,2	MCF-7	breast:
3	chr6:26245717..26248418-chr6:27832882..27834698,2	MCF-7	breast:
4	chr6:26270106..26271660-chr6:27833787..27835479,2	MCF-7	breast:
5	chr6:27832401..27835225-chr6:159419818..159422166,2	MCF-7	breast:
6	chr6:27119707..27122211-chr6:27833105..27834981,2	K562	blood:
7	chr6:25178946..25181215-chr6:27833164..27835187,2	MCF-7	breast:
8	chr1:11967132..11968839-chr6:27832941..27835901,2	MCF-7	breast:
9	chr6:26154866..26157028-chr6:27832028..27836151,3	MCF-7	breast:
10	chr6:26216342..26218938-chr6:27833572..27835102,2	MCF-7	breast:
11	chr10:75757407..75758102-chr6:27834148..27834733,2	Hela-S3	cervix:
12	chr6:27832725..27834714-chr6:27923810..27926804,2	K562	blood:
13	chr6:26249129..26252003-chr6:27832611..27836378,6	MCF-7	breast:
14	chr6:26271682..26274545-chr6:27832998..27834644,2	MCF-7	breast:
15	chr17:56735249..56737009-chr6:27834194..27835800,2	MCF-7	breast:
16	chr6:26156108..26158898-chr6:27832756..27836611,3	MCF-7	breast:
17	chr5:1522304..1524292-chr6:27832968..27834616,2	MCF-7	breast:
18	chr6:27099703..27101842-chr6:27833223..27835195,2	K562	blood:
19	chr6:27113081..27116777-chr6:27832860..27836046,4	K562	blood:
20	chr6:26033297..26035200-chr6:27833856..27836117,3	MCF-7	breast:
21	chr6:27105570..27109142-chr6:27832678..27836176,3	K562	blood:
22	chr6:26215814..26218576-chr6:27831262..27835058,4	K562	blood:
23	chr6:27098287..27101143-chr6:27833943..27835585,2	MCF-7	breast:
24	chr6:27832024..27834412-chr6:44214386..44216392,2	MCF-7	breast:
25	chr6:26044265..26046503-chr6:27834017..27836277,2	MCF-7	breast:
26	chr6:26019660..26022685-chr6:27833901..27836758,3	MCF-7	breast:
27	chr6:27833103..27835859-chr6:28582647..28584529,2	K562	blood:
28	chr6:27113591..27118417-chr6:27832860..27835856,7	K562	blood:
29	chr6:27832606..27835088-chr6:28302807..28304572,2	K562	blood:
30	chr1:149855909..149858308-chr6:27833822..27835971,2	MCF-7	breast:
31	chr17:56707936..56710461-chr6:27831380..27834313,2	MCF-7	breast:
32	chr6:27831507..27834483-chr6:28890233..28891763,2	MCF-7	breast:
33	chr6:26123458..26125812-chr6:27833699..27835902,2	K562	blood:
34	chr3:73160091..73160606-chr6:27834232..27834821,2	Hela-S3	cervix:
35	chr16:4663445..4665916-chr6:27834145..27836986,3	MCF-7	breast:
36	chr6:27113113..27117592-chr6:27831181..27837403,7	MCF-7	breast:
37	chr6:26033712..26035752-chr6:27832969..27835289,2	MCF-7	breast:
38	chr6:27832219..27835088-chr6:28302807..28305055,2	K562	blood:

No data

Variant related genes	Relation type
HIST1H2BPS2	TF binding region
ENSG00000153443	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000168242	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000256316	Chromatin interaction
ENSG00000130363	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000218690	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000124578	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000124657	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000035403	Chromatin interaction
ENSG00000256018	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000271913	Chromatin interaction
ENSG00000153395	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000163399	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs172083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs200487	0.84[MKK][hapmap]
rs200945	1.00[AMR][1000 genomes]
rs200957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs200960	1.00[AMR][1000 genomes]
rs602717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6902266	1.00[AMR][1000 genomes]

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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27830800-27835800	Active TSS	K562	blood
2	chr6:27831200-27835800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:27831200-27835800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:27831400-27834400	Active TSS	NHDF-Ad	bronchial
5	chr6:27831400-27835600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:27831600-27835400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr6:27831600-27835600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr6:27831600-27835800	Active TSS	Fetal Kidney	kidney
9	chr6:27831800-27834400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:27831800-27834400	Active TSS	Brain Substantia Nigra	brain
11	chr6:27831800-27834400	Active TSS	Fetal Intestine Large	intestine
12	chr6:27831800-27835400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:27831800-27835400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:27831800-27835400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr6:27831800-27835400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:27831800-27835400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:27831800-27835600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr6:27831800-27835600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr6:27831800-27835800	Active TSS	Aorta	Aorta
20	chr6:27832000-27835400	Flanking Active TSS	Liver	Liver
21	chr6:27832000-27835400	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr6:27832000-27835600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:27832200-27834400	Active TSS	Small Intestine	intestine
24	chr6:27832200-27834400	Active TSS	GM12878-XiMat	blood
25	chr6:27832200-27834400	Active TSS	HSMMtube	muscle
26	chr6:27832200-27835400	Active TSS	Esophagus	oesophagus
27	chr6:27832200-27835600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:27832200-27835600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:27832200-27836000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:27832400-27834400	Active TSS	Stomach Mucosa	stomach
31	chr6:27832400-27834600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:27832400-27835400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
33	chr6:27832600-27834400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:27832600-27834400	Active TSS	Fetal Stomach	stomach
35	chr6:27832600-27835600	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr6:27832600-27835600	Active TSS	Dnd41	blood
37	chr6:27832800-27835600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:27832800-27835800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:27832800-27835800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:27833000-27835400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:27833000-27835400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:27833000-27835400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:27833000-27835400	Transcr. at gene 5' and 3'	Right Atrium	heart
44	chr6:27833000-27835400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
45	chr6:27833000-27835600	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr6:27833000-27835600	Active TSS	Hela-S3	cervix
47	chr6:27833000-27835800	Active TSS	H1 Cell Line	embryonic stem cell
48	chr6:27833000-27835800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr6:27833200-27834800	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
50	chr6:27833200-27835000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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