Variant report

Variant	rs73501629
Chromosome Location	chr6:87862209-87862210
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	NFIC	chr6:87861463-87862605	GM12878	blood:	n/a	n/a
2	MAX	chr6:87861623-87862245	MCF-7	breast:	n/a	chr6:87862031-87862041
3	POLR2A	chr6:87861210-87863425	GM12891	blood:	n/a	n/a
4	POLR2A	chr6:87861390-87862355	GM12878	blood:	n/a	n/a
5	MXI1	chr6:87861831-87862344	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr6:87861209-87862480	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:87861353-87862415	GM12892	blood:	n/a	n/a
8	MAX	chr6:87861197-87862462	GM12878	blood:	n/a	chr6:87862031-87862041
9	GTF2F1	chr6:87861341-87862299	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:87861302-87862300	Gliobla	brain:	n/a	n/a
11	YY1	chr6:87861325-87862299	GM12892	blood:	n/a	chr6:87861581-87861595 chr6:87862114-87862128 chr6:87862037-87862048
12	REST	chr6:87861087-87862586	H1-neurons	neurons:	n/a	chr6:87861585-87861595
13	STAT5A	chr6:87861611-87862742	GM12878	blood:	n/a	n/a
14	TAF1	chr6:87861364-87862332	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr6:87861328-87862606	SK-N-SH	brain:	n/a	chr6:87862031-87862041
16	POLR2A	chr6:87861324-87862560	PANC-1	pancreas:	n/a	n/a
17	RCOR1	chr6:87861168-87862574	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:87861348-87862623	GM12878	blood:	n/a	n/a
19	YY1	chr6:87861300-87862390	SK-N-SH_RA	brain:	n/a	chr6:87861581-87861595 chr6:87862114-87862128 chr6:87862037-87862048
20	POLR2A	chr6:87861481-87862352	H1-neurons	neurons:	n/a	n/a
21	TAF1	chr6:87861249-87862406	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr6:87861388-87862314	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAZ	chr6:87861328-87862672	GM12878	blood:	n/a	chr6:87862031-87862041
24	POLR2A	chr6:87861456-87862230	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr6:87861161-87862704	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:87861114-87862547	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:87861645-87862349	MCF-7	breast:	n/a	n/a
28	POLR2A	chr6:87861634-87862475	GM12892	blood:	n/a	n/a
29	POLR2A	chr6:87861516-87862360	GM12891	blood:	n/a	n/a
30	POLR2A	chr6:87861233-87862702	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr6:87861264-87862945	GM19099	blood:	n/a	n/a
32	BHLHE40	chr6:87861139-87862710	GM12878	blood:	n/a	chr6:87861585-87861601
33	POLR2A	chr6:87861433-87862398	IMR90	lung:	n/a	n/a
34	BCLAF1	chr6:87861428-87862334	GM12878	blood:	n/a	chr6:87861592-87861601 chr6:87861960-87861968 chr6:87862035-87862048 chr6:87861583-87861596
35	MAX	chr6:87861258-87862231	ECC-1	luminal epithelium:	n/a	chr6:87862031-87862041
36	STAT1	chr6:87861874-87862635	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:87861216-87862359	PANC-1	pancreas:	n/a	n/a
38	MAX	chr6:87861418-87862531	SK-N-SH	brain:	n/a	chr6:87862031-87862041
39	ELF1	chr6:87861252-87862372	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:87861486-87862230	HUVEC	blood vessel:	n/a	n/a
41	WRNIP1	chr6:87861948-87862688	GM12878	blood:	n/a	n/a
42	ELF1	chr6:87861339-87862533	GM12878	blood:	n/a	n/a
43	CHD2	chr6:87861214-87862623	GM12878	blood:	n/a	n/a
44	MAX	chr6:87861914-87862465	H1-hESC	embryonic stem cell:	n/a	chr6:87862031-87862041
45	TEAD4	chr6:87861983-87862348	H1-hESC	embryonic stem cell:	n/a	n/a
46	STAT3	chr6:87862112-87862412	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr6:87861309-87862352	U87	brain:	n/a	n/a
48	STAT3	chr6:87862153-87862435	MCF10A-Er-Src	breast:	n/a	n/a
49	FOXM1	chr6:87861229-87862245	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:87861393-87862324	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:87860967..87863617-chr6:87863794..87865835,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CGA-2	chr6:87860877-87865003	ENSG00000272008.1

Variant related genes	Relation type
ZNF292	TF binding region
ENSG00000188994	Chromatin interaction
ENSG00000272008	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10488045	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10498960	0.88[EUR][1000 genomes]
rs16878473	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16878570	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878638	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878712	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878713	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878729	0.91[EUR][1000 genomes]
rs16878734	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878736	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878809	0.82[EUR][1000 genomes]
rs16878856	0.88[EUR][1000 genomes]
rs16878863	0.88[EUR][1000 genomes]
rs16878942	0.88[EUR][1000 genomes]
rs1925693	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41273281	0.88[EUR][1000 genomes]
rs41273283	0.88[EUR][1000 genomes]
rs55647962	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs56096438	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56193950	0.88[EUR][1000 genomes]
rs56678817	0.88[EUR][1000 genomes]
rs56743579	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56847789	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56947685	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56999910	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57043501	0.88[EUR][1000 genomes]
rs57116567	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57217108	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57421283	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57607342	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57962992	0.97[EUR][1000 genomes]
rs58032842	1.00[AMR][1000 genomes]
rs58124219	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58269367	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58327183	0.88[EUR][1000 genomes]
rs58474842	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58576901	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58731649	0.88[EUR][1000 genomes]
rs58735749	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58751410	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59034165	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59138817	0.88[EUR][1000 genomes]
rs59150116	0.88[EUR][1000 genomes]
rs59214037	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59344869	0.95[AFR][1000 genomes]
rs59495279	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59654654	0.87[EUR][1000 genomes]
rs59875769	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59964119	1.00[AMR][1000 genomes]
rs60074363	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60285195	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60544317	0.85[EUR][1000 genomes]
rs60746078	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60845773	0.88[EUR][1000 genomes]
rs60985818	0.94[EUR][1000 genomes]
rs60994855	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61047847	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61379368	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61705669	0.88[EUR][1000 genomes]
rs73483720	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483728	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483743	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483749	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483752	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483758	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483760	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483765	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483769	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483771	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73483774	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483790	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483796	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483799	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485808	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485811	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73485813	0.94[EUR][1000 genomes]
rs73485815	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73485820	0.88[EUR][1000 genomes]
rs73485826	0.88[EUR][1000 genomes]
rs73485828	0.88[EUR][1000 genomes]
rs73485831	0.88[EUR][1000 genomes]
rs73485848	0.88[EUR][1000 genomes]
rs73485849	0.88[EUR][1000 genomes]
rs73499768	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73499770	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73499771	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73499800	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73499802	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501611	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73501620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501632	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501636	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501638	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501641	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501658	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501662	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73751992	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv604114	chr6:87816905-87906053	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv3366503	chr6:87849282-87862940	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87860800-87862400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:87860800-87862800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:87861000-87862400	Active TSS	Fetal Brain Female	brain
4	chr6:87861000-87863200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:87861000-87866200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:87861200-87862400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:87861200-87862400	Flanking Active TSS	Colonic Mucosa	Colon
8	chr6:87861200-87862400	Active TSS	Fetal Lung	lung
9	chr6:87861200-87862400	Active TSS	Fetal Stomach	stomach
10	chr6:87861200-87862600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr6:87861200-87862600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:87861200-87862600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr6:87861200-87862600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:87861200-87862600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr6:87861200-87862600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr6:87861200-87862600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr6:87861200-87862600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:87861200-87862600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:87861200-87862600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:87861200-87862600	Active TSS	Brain Germinal Matrix	brain
21	chr6:87861200-87862600	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr6:87861200-87862600	Active TSS	Fetal Kidney	kidney
23	chr6:87861200-87862600	Active TSS	Ovary	ovary
24	chr6:87861200-87862600	Active TSS	Right Ventricle	heart
25	chr6:87861200-87862600	Active TSS	HSMMtube	muscle
26	chr6:87861200-87862600	Flanking Active TSS	HUVEC	blood vessel
27	chr6:87861200-87862800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:87861200-87862800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:87861200-87862800	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr6:87861200-87862800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr6:87861200-87862800	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr6:87861200-87862800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr6:87861200-87862800	Active TSS	Brain Angular Gyrus	brain
34	chr6:87861200-87862800	Active TSS	Brain Substantia Nigra	brain
35	chr6:87861200-87862800	Active TSS	Psoas Muscle	Psoas
36	chr6:87861200-87862800	Active TSS	Right Atrium	heart
37	chr6:87861200-87863000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:87861200-87863000	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr6:87861200-87863000	Flanking Active TSS	HMEC	breast
40	chr6:87861200-87863200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr6:87861200-87866600	Active TSS	Aorta	Aorta
42	chr6:87861200-87866600	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr6:87861400-87862400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:87861400-87862400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:87861400-87862400	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr6:87861400-87862400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr6:87861400-87862400	Active TSS	Brain Cingulate Gyrus	brain
48	chr6:87861400-87862400	Active TSS	Osteobl	bone
49	chr6:87861400-87862600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr6:87861400-87862600	Flanking Active TSS	Primary B cells from cord blood	blood

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