Variant report

Variant	rs11753610
Chromosome Location	chr6:26251601-26251602
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	SIN3AK20	chr6:26251449-26252306	MCF-7	breast:	n/a	n/a
2	MXI1	chr6:26251512-26252615	IMR90	lung:	n/a	n/a
3	RXRA	chr6:26251459-26252050	GM12878	blood:	n/a	n/a
4	NFIC	chr6:26251435-26252590	GM12878	blood:	n/a	n/a
5	NFYB	chr6:26250969-26251890	Hela-S3	cervix:	n/a	chr6:26251178-26251190 chr6:26251742-26251756 chr6:26251708-26251722 chr6:26251176-26251191 chr6:26251177-26251187
6	CHD2	chr6:26251563-26252232	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:26251500-26252711	HUVEC	blood vessel:	n/a	n/a
8	ZNF143	chr6:26251515-26252038	GM12878	blood:	n/a	chr6:26251670-26251679
9	TBL1XR1	chr6:26251533-26252496	GM12878	blood:	n/a	n/a
10	EBF1	chr6:26251526-26251848	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:26251600-26252740	HUVEC	blood vessel:	n/a	n/a
12	CREB1	chr6:26251568-26252067	H1-hESC	embryonic stem cell:	n/a	n/a
13	CEBPB	chr6:26251584-26252503	GM12878	blood:	n/a	n/a
14	FOXM1	chr6:26251524-26252656	GM12878	blood:	n/a	n/a
15	TAF1	chr6:26251543-26252578	H1-hESC	embryonic stem cell:	n/a	n/a
16	EP300	chr6:26251518-26252095	SK-N-SH	brain:	n/a	n/a
17	STAT3	chr6:26251590-26251985	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr6:26251599-26252913	GM12892	blood:	n/a	n/a
19	TCF12	chr6:26251518-26252294	SK-N-SH	brain:	n/a	chr6:26251819-26251826
20	EBF1	chr6:26251433-26251998	GM12878	blood:	n/a	n/a
21	NFIC	chr6:26249305-26253014	GM12878	blood:	n/a	n/a
22	MAZ	chr6:26251600-26252096	GM12878	blood:	n/a	n/a
23	TBP	chr6:26251520-26252035	GM12878	blood:	n/a	n/a
24	ARID3A	chr6:26251559-26251966	K562	blood:	n/a	n/a
25	POLR2A	chr6:26251516-26253362	GM12892	blood:	n/a	n/a
26	SP1	chr6:26251425-26252105	H1-hESC	embryonic stem cell:	n/a	chr6:26251734-26251755
27	NFATC1	chr6:26251546-26252775	GM12878	blood:	n/a	n/a
28	SP1	chr6:26251505-26252025	K562	blood:	n/a	chr6:26251734-26251755
29	ELF1	chr6:26251212-26251879	MCF-7	breast:	n/a	n/a
30	CBX3	chr6:26251466-26252008	K562	blood:	n/a	n/a
31	POU2F2	chr6:26251572-26252304	GM12878	blood:	n/a	chr6:26251791-26251801 chr6:26251792-26251803 chr6:26251792-26251801 chr6:26251793-26251801 chr6:26251792-26251802 chr6:26251789-26251804 chr6:26251793-26251800 chr6:26251788-26251806
32	TBP	chr6:26251596-26252007	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr6:26251576-26252171	MCF10A-Er-Src	breast:	n/a	n/a
34	NFYA	chr6:26250769-26251899	GM12878	blood:	n/a	chr6:26250906-26250921 chr6:26251178-26251190 chr6:26251742-26251756 chr6:26250909-26250919 chr6:26251737-26251755 chr6:26250906-26250921 chr6:26250907-26250921 chr6:26251757-26251775 chr6:26251708-26251722 chr6:26251177-26251187
35	POU2F2	chr6:26251523-26252734	GM12878	blood:	n/a	chr6:26251791-26251801 chr6:26251792-26251803 chr6:26251792-26251801 chr6:26251793-26251801 chr6:26251792-26251802 chr6:26251789-26251804 chr6:26251793-26251800 chr6:26251788-26251806
36	RELA	chr6:26251386-26252594	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:26251505-26252955	U87	brain:	n/a	n/a
38	RELA	chr6:26251568-26252603	GM18951	blood:	n/a	n/a
39	TAF7	chr6:26251360-26254160	H1-hESC	embryonic stem cell:	n/a	n/a
40	CHD1	chr6:26251380-26252680	GM12878	blood:	n/a	n/a
41	IRF3	chr6:26251569-26252029	Hela-S3	cervix:	n/a	chr6:26251745-26251754
42	POLR2A	chr6:26251589-26252422	MCF-7	breast:	n/a	n/a
43	POLR2A	chr6:26249056-26254440	H1-hESC	embryonic stem cell:	n/a	n/a
44	PML	chr6:26251377-26253053	GM12878	blood:	n/a	n/a
45	CHD1	chr6:26249456-26253189	IMR90	lung:	n/a	n/a
46	MTA3	chr6:26251566-26252812	GM12878	blood:	n/a	n/a
47	POLR2A	chr6:26251596-26252802	ProgFib	skin:	n/a	n/a
48	POLR2A	chr6:26251469-26253771	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr6:26251536-26252811	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr6:26251583-26253307	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26250131..26252759-chr9:103947028..103949743,2	MCF-7	breast:
2	chr6:26251588..26253194-chr6:27805528..27807609,2	MCF-7	breast:
3	chr6:26250835..26253676-chr6:27791814..27793929,3	MCF-7	breast:
4	chr6:26248591..26251636-chr6:26519454..26522320,3	K562	blood:
5	chr6:26251146..26253311-chr6:27798112..27799639,2	MCF-7	breast:
6	chr6:26251055..26254665-chr6:27113819..27116327,4	MCF-7	breast:
7	chr20:55838553..55841371-chr6:26249456..26251854,2	MCF-7	breast:
8	chr6:26249129..26252003-chr6:27832611..27836378,6	MCF-7	breast:
9	chr6:26250350..26252961-chr6:27100694..27103484,2	K562	blood:
10	chr5:175962855..175964855-chr6:26250361..26252546,2	MCF-7	breast:
11	chr17:59475732..59477627-chr6:26249790..26252547,2	MCF-7	breast:
12	chr6:26248843..26252508-chr6:27859565..27863258,4	K562	blood:
13	chr6:26032854..26035580-chr6:26251207..26253979,3	MCF-7	breast:
14	chr6:26248241..26251766-chr6:27097726..27103043,5	MCF-7	breast:
15	chr6:26251387..26252142-chr7:100472118..100473007,2	Hela-S3	cervix:

Variant related genes	Relation type
HIST1H2BH	TF binding region
HIST1H3F	TF binding region
HIST1H4G	TF binding region
ENSG00000199289	Chromatin interaction
ENSG00000148123	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000197238	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000087087	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000146083	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000184357	Chromatin interaction
ENSG00000198374	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197914	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000137259	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11751062	1.00[CHD][hapmap];0.91[GIH][hapmap]
rs11751286	0.80[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11754368	1.00[CHD][hapmap];0.91[GIH][hapmap]
rs11755618	1.00[CHD][hapmap];0.91[GIH][hapmap]
rs11757549	0.86[GIH][hapmap]
rs11759720	0.81[GIH][hapmap]
rs16891464	1.00[CHD][hapmap];0.91[GIH][hapmap]
rs16891484	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1741738	1.00[LWK][hapmap]
rs17531978	1.00[LWK][hapmap]
rs3734534	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41266821	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
8	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
9	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
10	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
11	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
12	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
13	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
14	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
15	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases
16	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11753610	HIST1H3E	cis	parietal	SCAN
rs11753610	HIST1H3E	cis	cerebellum	SCAN
rs11753610	HIST1H3E	Cis_1M	lymphoblastoid	RTeQTL
rs11753610	ZKSCAN4	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26249200-26251800	Active TSS	Brain Germinal Matrix	brain
2	chr6:26249200-26254000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:26249200-26254200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:26249200-26254600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr6:26249400-26252000	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr6:26249400-26252400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
7	chr6:26249400-26252600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr6:26249400-26253000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr6:26249400-26253200	Active TSS	Fetal Lung	lung
10	chr6:26249400-26253400	Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr6:26249400-26253400	Active TSS	K562	blood
12	chr6:26249400-26254000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:26249400-26254000	Active TSS	Fetal Kidney	kidney
14	chr6:26249400-26254200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:26249400-26254200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:26249400-26254200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:26249400-26254200	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr6:26249400-26254200	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr6:26249400-26254200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:26249600-26252000	Active TSS	Placenta	Placenta
21	chr6:26249600-26252400	Active TSS	Fetal Heart	heart
22	chr6:26249600-26253400	Active TSS	Fetal Brain Female	brain
23	chr6:26249600-26253600	Active TSS	Duodenum Mucosa	Duodenum
24	chr6:26249600-26253800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:26249600-26253800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
26	chr6:26249600-26254000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:26249600-26254000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:26249600-26254000	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr6:26249600-26254000	Active TSS	GM12878-XiMat	blood
30	chr6:26249600-26254200	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr6:26249600-26254200	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr6:26249600-26254200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:26249600-26254200	Active TSS	Fetal Stomach	stomach
34	chr6:26249600-26254200	Active TSS	NHLF	lung
35	chr6:26249600-26254800	Active TSS	Thymus	Thymus
36	chr6:26249600-26255400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:26249800-26252000	Active TSS	Fetal Muscle Leg	muscle
38	chr6:26249800-26252200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:26249800-26252400	Active TSS	Aorta	Aorta
40	chr6:26249800-26252400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
41	chr6:26249800-26252400	Active TSS	Placenta Amnion	Placenta Amnion
42	chr6:26249800-26252600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
43	chr6:26249800-26252600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
44	chr6:26249800-26252800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:26249800-26253000	Active TSS	Primary B cells from peripheral blood	blood
46	chr6:26249800-26253000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr6:26249800-26253000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:26249800-26253200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr6:26249800-26253400	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr6:26249800-26253800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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