Variant report

Variant	rs6587206
Chromosome Location	chr17:19881587-19881588
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	USF2	chr17:19881067-19881737	H1-hESC	embryonic stem cell:	n/a	chr17:19881241-19881252 chr17:19881207-19881223
2	POLR2A	chr17:19880578-19881710	K562	blood:	n/a	n/a
3	MAX	chr17:19880509-19881877	GM12878	blood:	n/a	chr17:19881241-19881252 chr17:19881244-19881260 chr17:19881240-19881249 chr17:19881242-19881251
4	MAX	chr17:19880430-19881800	HCT-116	colon:	n/a	chr17:19880497-19880504 chr17:19881241-19881252 chr17:19881244-19881260 chr17:19881240-19881249 chr17:19881242-19881251
5	EP300	chr17:19881587-19881756	GM12878	blood:	n/a	n/a
6	REST	chr17:19880403-19882013	H1-neurons	neurons:	n/a	chr17:19881684-19881694
7	CHD2	chr17:19880934-19882060	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F6	chr17:19880973-19881736	K562	blood:	n/a	chr17:19881039-19881046 chr17:19881039-19881046 chr17:19881181-19881191 chr17:19881039-19881046
9	RELA	chr17:19880459-19881848	GM10847	blood:	n/a	n/a
10	USF1	chr17:19880904-19881712	HCT-116	colon:	n/a	chr17:19881241-19881252 chr17:19881207-19881223
11	BCLAF1	chr17:19880800-19881816	GM12878	blood:	n/a	chr17:19880881-19880894 chr17:19880854-19880863 chr17:19880824-19880833
12	POLR2A	chr17:19880574-19881779	GM12891	blood:	n/a	n/a
13	REST	chr17:19880354-19882109	A549	lung:	n/a	chr17:19881684-19881694
14	YY1	chr17:19880434-19881697	SK-N-SH	brain:	n/a	chr17:19880882-19880896 chr17:19881105-19881117 chr17:19881337-19881351 chr17:19881106-19881128 chr17:19881106-19881116 chr17:19880852-19880863
15	POLR2A	chr17:19880455-19881774	GM12892	blood:	n/a	n/a
16	POLR2A	chr17:19880115-19882375	GM12891	blood:	n/a	n/a
17	POLR2A	chr17:19880545-19882178	GM19099	blood:	n/a	n/a
18	BHLHE40	chr17:19880952-19882354	GM12878	blood:	n/a	chr17:19881207-19881223
19	SPI1	chr17:19881487-19881917	GM12891	blood:	n/a	chr17:19881708-19881721
20	MAX	chr17:19880527-19881613	SK-N-SH	brain:	n/a	chr17:19881241-19881252 chr17:19881244-19881260 chr17:19881240-19881249 chr17:19881242-19881251
21	MTA3	chr17:19881327-19881837	GM12878	blood:	n/a	n/a
22	MAX	chr17:19880443-19882108	NB4	blood:	n/a	chr17:19880497-19880504 chr17:19881241-19881252 chr17:19881244-19881260 chr17:19881240-19881249 chr17:19881242-19881251 chr17:19882034-19882043
23	POLR2A	chr17:19879996-19884397	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAZ	chr17:19880899-19881617	Hela-S3	cervix:	n/a	chr17:19881241-19881252 chr17:19881244-19881260 chr17:19881240-19881249 chr17:19881242-19881251
25	TBP	chr17:19880954-19881788	GM12878	blood:	n/a	n/a
26	SRF	chr17:19881517-19881779	GM12878	blood:	n/a	n/a
27	E2F6	chr17:19880726-19881653	A549	lung:	n/a	chr17:19881039-19881046 chr17:19881039-19881046 chr17:19881181-19881191 chr17:19880907-19880922 chr17:19881039-19881046 chr17:19880881-19880890 chr17:19880885-19880895
28	POLR2A	chr17:19880596-19881794	MCF-7	breast:	n/a	n/a
29	RELA	chr17:19880191-19881870	GM19099	blood:	n/a	n/a
30	EBF1	chr17:19881032-19881790	GM12878	blood:	n/a	n/a
31	USF1	chr17:19881061-19881629	GM12878	blood:	n/a	chr17:19881241-19881252 chr17:19881207-19881223
32	MAX	chr17:19880535-19881635	Hela-S3	cervix:	n/a	chr17:19881241-19881252 chr17:19881244-19881260 chr17:19881240-19881249 chr17:19881242-19881251
33	PAX5	chr17:19881462-19881747	GM12878	blood:	n/a	n/a
34	TCF12	chr17:19880084-19881845	A549	lung:	n/a	chr17:19880842-19880852
35	POLR2A	chr17:19880230-19881912	PBDE	blood:	n/a	n/a
36	ELF1	chr17:19880722-19881809	K562	blood:	n/a	chr17:19881386-19881398 chr17:19881009-19881018 chr17:19881336-19881348 chr17:19881008-19881019
37	CHD1	chr17:19880221-19881777	GM12878	blood:	n/a	chr17:19880440-19880450
38	IRF1	chr17:19880956-19881698	K562	blood:	n/a	chr17:19881182-19881196
39	SP1	chr17:19880764-19881799	A549	lung:	n/a	chr17:19881185-19881195 chr17:19881185-19881199 chr17:19881190-19881197 chr17:19881184-19881196 chr17:19881186-19881195 chr17:19881185-19881194 chr17:19881416-19881428 chr17:19881184-19881196 chr17:19881199-19881213 chr17:19881185-19881194 chr17:19881418-19881427 chr17:19881416-19881428 chr17:19881185-19881195
40	POLR2A	chr17:19880400-19881845	GM12878	blood:	n/a	n/a
41	CHD2	chr17:19880415-19882004	GM12878	blood:	n/a	chr17:19880440-19880450
42	POLR2A	chr17:19880454-19881669	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr17:19880638-19881881	HL-60	blood:	n/a	n/a
44	MXI1	chr17:19880021-19882329	SK-N-SH	brain:	n/a	chr17:19881243-19881252 chr17:19880842-19880851
45	MXI1	chr17:19880208-19882018	IMR90	lung:	n/a	chr17:19881243-19881252 chr17:19880842-19880851
46	MTA3	chr17:19880470-19882264	GM12878	blood:	n/a	n/a
47	ELF1	chr17:19880625-19881640	HCT-116	colon:	n/a	chr17:19881386-19881398 chr17:19881009-19881018 chr17:19881336-19881348 chr17:19881008-19881019
48	POLR2A	chr17:19880594-19881899	K562	blood:	n/a	n/a
49	POLR2A	chr17:19880550-19881995	GM18526	blood:	n/a	n/a
50	REST	chr17:19880831-19881630	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19834831..19836752-chr17:19879517..19881756,2	MCF-7	breast:
2	chr17:19881500..19882356-chr17:74553533..74554276,2	NB4	blood:
3	chr17:19769754..19773058-chr17:19878983..19882883,4	MCF-7	breast:
4	chr17:19879148..19882537-chr17:19911149..19913260,3	MCF-7	breast:
5	chr17:19769588..19772074-chr17:19879592..19882526,4	MCF-7	breast:
6	chr17:19861091..19865827-chr17:19879221..19882528,6	MCF-7	breast:
7	chr17:19878871..19883594-chr17:20057277..20060362,4	K562	blood:
8	chr17:19881019..19882535-chr17:19912703..19915442,2	K562	blood:
9	chr17:19880813..19883681-chr17:19988880..19990706,2	MCF-7	breast:

Variant related genes	Relation type
AKAP10	TF binding region
ENSG00000108599	Chromatin interaction
ENSG00000267546	Chromatin interaction
ENSG00000083290	Chromatin interaction
ENSG00000163597	Chromatin interaction
ENSG00000128487	Chromatin interaction
ENSG00000261033	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11204419	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204420	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204421	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs119672	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1479129	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1638525	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs169412	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs169414	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs175921	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs175922	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs191865	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203450	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203451	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203452	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203455	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs203456	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203457	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203458	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203459	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs203460	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203461	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203462	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203465	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203466	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203469	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs203470	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203477	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203479	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203481	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203482	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2108978	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108980	0.80[AFR][1000 genomes]
rs397969	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs427798	0.80[EUR][1000 genomes]
rs4479308	0.84[ASN][1000 genomes]
rs4925060	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56153261	0.84[ASN][1000 genomes]
rs7222403	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066150	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs850623	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860335	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9907752	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9914273	0.81[EUR][1000 genomes]
rs9916675	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6587206	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19879200-19881600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr17:19879400-19882000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr17:19879400-19882400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr17:19879600-19881600	Active TSS	HSMM	muscle
5	chr17:19879600-19881800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:19880000-19881600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr17:19880000-19881600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr17:19880000-19881600	Active TSS	Fetal Intestine Large	intestine
9	chr17:19880000-19881600	Active TSS	Fetal Intestine Small	intestine
10	chr17:19880000-19881600	Active TSS	Gastric	stomach
11	chr17:19880000-19881600	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr17:19880000-19881800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr17:19880000-19882000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr17:19880000-19882000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr17:19880000-19882200	Active TSS	Fetal Lung	lung
16	chr17:19880000-19882400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr17:19880000-19882400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr17:19880000-19884000	Active TSS	H1 Cell Line	embryonic stem cell
19	chr17:19880200-19881600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr17:19880200-19881600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:19880200-19881600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr17:19880200-19881600	Active TSS	Esophagus	oesophagus
23	chr17:19880200-19881600	Active TSS	Left Ventricle	heart
24	chr17:19880200-19881600	Active TSS	Placenta Amnion	Placenta Amnion
25	chr17:19880200-19881600	Active TSS	Psoas Muscle	Psoas
26	chr17:19880200-19881600	Active TSS	Stomach Mucosa	stomach
27	chr17:19880200-19881800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:19880200-19881800	Active TSS	Aorta	Aorta
29	chr17:19880200-19881800	Active TSS	Thymus	Thymus
30	chr17:19880200-19882000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr17:19880200-19882000	Active TSS	Fetal Kidney	kidney
32	chr17:19880200-19882400	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr17:19880200-19884400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr17:19880400-19881600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:19880400-19881600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr17:19880400-19881600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr17:19880400-19881600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr17:19880400-19881600	Active TSS	Brain Hippocampus Middle	brain
39	chr17:19880400-19881600	Active TSS	Brain Substantia Nigra	brain
40	chr17:19880400-19881600	Active TSS	Colon Smooth Muscle	Colon
41	chr17:19880400-19881600	Active TSS	Fetal Heart	heart
42	chr17:19880400-19881600	Active TSS	Fetal Muscle Leg	muscle
43	chr17:19880400-19881600	Active TSS	Fetal Stomach	stomach
44	chr17:19880400-19881600	Active TSS	Right Ventricle	heart
45	chr17:19880400-19881600	Active TSS	Stomach Smooth Muscle	stomach
46	chr17:19880400-19881800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr17:19880400-19881800	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr17:19880400-19881800	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr17:19880400-19881800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr17:19880400-19881800	Active TSS	Ovary	ovary

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