Variant report

Variant	rs12975585
Chromosome Location	chr19:41770231-41770232
allele	A/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	E2F4	chr19:41769101-41770367	GM12878	blood:	n/a	chr19:41770065-41770076 chr19:41770066-41770074 chr19:41769863-41769875 chr19:41770066-41770078 chr19:41770066-41770075 chr19:41770168-41770177 chr19:41770016-41770026 chr19:41770062-41770077 chr19:41770067-41770074 chr19:41770067-41770074 chr19:41770067-41770074
2	YY1	chr19:41769666-41770640	NT2-D1	testis:	n/a	chr19:41770267-41770276 chr19:41770274-41770282 chr19:41770270-41770282 chr19:41770271-41770281 chr19:41770262-41770276 chr19:41770271-41770293
3	POU2F2	chr19:41768718-41770350	GM12891	blood:	n/a	chr19:41770072-41770084 chr19:41769995-41770005
4	SP1	chr19:41768794-41770564	GM12878	blood:	n/a	chr19:41770157-41770178 chr19:41769743-41769755 chr19:41770051-41770065 chr19:41769814-41769835 chr19:41769745-41769754 chr19:41770050-41770062
5	SP1	chr19:41768812-41771402	HCT-116	colon:	n/a	chr19:41770157-41770178 chr19:41770908-41770917 chr19:41771123-41771132 chr19:41769743-41769755 chr19:41770714-41770726 chr19:41771119-41771133 chr19:41770051-41770065 chr19:41770903-41770917 chr19:41770906-41770918 chr19:41769814-41769835 chr19:41770716-41770725 chr19:41770902-41770915 chr19:41770907-41770917 chr19:41769745-41769754 chr19:41770907-41770916 chr19:41770050-41770062 chr19:41770714-41770726 chr19:41770715-41770724 chr19:41770906-41770918
6	NFYB	chr19:41769356-41770437	GM12878	blood:	n/a	chr19:41770033-41770046 chr19:41770167-41770177 chr19:41770166-41770179 chr19:41770164-41770179 chr19:41770164-41770179 chr19:41769999-41770014 chr19:41769969-41769984 chr19:41770168-41770180 chr19:41770167-41770177 chr19:41770165-41770179
7	REST	chr19:41770030-41771205	HL-60	blood:	n/a	chr19:41770353-41770362
8	MAX	chr19:41768957-41770333	Hela-S3	cervix:	n/a	chr19:41770252-41770262
9	E2F6	chr19:41769701-41770308	K562	blood:	n/a	chr19:41770066-41770074 chr19:41769863-41769875 chr19:41770066-41770078 chr19:41770066-41770075 chr19:41770168-41770177 chr19:41770016-41770026 chr19:41770062-41770077 chr19:41770067-41770074 chr19:41770065-41770076 chr19:41770067-41770074 chr19:41770067-41770074
10	MTA3	chr19:41770029-41770477	GM12878	blood:	n/a	n/a
11	NRF1	chr19:41769452-41770240	GM12878	blood:	n/a	n/a
12	MAX	chr19:41769561-41770787	K562	blood:	n/a	chr19:41770252-41770262
13	ATF2	chr19:41768854-41770487	GM12878	blood:	n/a	n/a
14	MYC	chr19:41769961-41770382	HUVEC	blood vessel:	n/a	chr19:41770252-41770262
15	RELA	chr19:41768979-41770451	GM18505	blood:	n/a	n/a
16	POLR2A	chr19:41768093-41771218	Raji	blood:	n/a	n/a
17	ELK1	chr19:41769150-41770535	K562	blood:	n/a	n/a
18	REST	chr19:41770004-41770710	HepG2	liver:	n/a	chr19:41770353-41770362
19	UBTF	chr19:41769980-41772007	K562	blood:	n/a	n/a
20	EGR1	chr19:41769917-41770531	MCF-7	breast:	n/a	n/a
21	FOXA1	chr19:41769472-41770447	HepG2	liver:	n/a	n/a
22	SP1	chr19:41769327-41770339	K562	blood:	n/a	chr19:41770157-41770178 chr19:41769743-41769755 chr19:41770051-41770065 chr19:41769814-41769835 chr19:41769745-41769754 chr19:41770050-41770062
23	PAX5	chr19:41768836-41770310	GM12878	blood:	n/a	n/a
24	GABPA	chr19:41769517-41770626	K562	blood:	n/a	n/a
25	EP300	chr19:41768903-41770371	K562	blood:	n/a	chr19:41770071-41770087
26	POLR2A	chr19:41769975-41771300	H1-neurons	neurons:	n/a	n/a
27	YY1	chr19:41769466-41770957	K562	blood:	n/a	chr19:41770267-41770276 chr19:41770722-41770733 chr19:41770274-41770282 chr19:41770270-41770282 chr19:41770271-41770281 chr19:41770262-41770276 chr19:41770271-41770293 chr19:41770712-41770726
28	FOXM1	chr19:41769494-41770540	MCF-7	breast:	n/a	n/a
29	MXI1	chr19:41769439-41770280	K562	blood:	n/a	chr19:41770147-41770162
30	USF2	chr19:41769672-41770405	H1-hESC	embryonic stem cell:	n/a	n/a
31	ELK4	chr19:41769610-41770273	HEK293	kidney:	n/a	n/a
32	GABPA	chr19:41768947-41771242	A549	lung:	n/a	n/a
33	ZKSCAN1	chr19:41769400-41770585	Hela-S3	cervix:	n/a	n/a
34	SP2	chr19:41769777-41770277	K562	blood:	n/a	chr19:41770166-41770176 chr19:41769862-41769871
35	POLR2A	chr19:41768085-41771893	GM19193	blood:	n/a	n/a
36	TBP	chr19:41768989-41772071	K562	blood:	n/a	n/a
37	MTA3	chr19:41768794-41771880	GM12878	blood:	n/a	n/a
38	UBTF	chr19:41770178-41771019	K562	blood:	n/a	n/a
39	MYC	chr19:41768923-41771027	K562	blood:	n/a	chr19:41770252-41770262
40	MYC	chr19:41768970-41771026	K562	blood:	n/a	chr19:41770252-41770262
41	ELK1	chr19:41769500-41770394	Hela-S3	cervix:	n/a	n/a
42	TAF1	chr19:41769995-41770569	MCF-7	breast:	n/a	n/a
43	RFX5	chr19:41768867-41771382	SK-N-SH	brain:	n/a	chr19:41769824-41769833 chr19:41770167-41770176
44	JUND	chr19:41768915-41772213	A549	lung:	n/a	chr19:41770714-41770723 chr19:41769880-41769889 chr19:41769949-41769961 chr19:41770306-41770315 chr19:41770166-41770175 chr19:41769082-41769093
45	ELF1	chr19:41769466-41770435	K562	blood:	n/a	chr19:41770081-41770093 chr19:41770286-41770295 chr19:41770262-41770274
46	BHLHE40	chr19:41768890-41770683	GM12878	blood:	n/a	n/a
47	USF1	chr19:41769250-41770375	A549	lung:	n/a	n/a
48	ELF1	chr19:41769569-41771653	GM12878	blood:	n/a	chr19:41770081-41770093 chr19:41770286-41770295 chr19:41770719-41770731 chr19:41770262-41770274
49	POLR2A	chr19:41767388-41771764	U87	brain:	n/a	n/a
50	POLR2A	chr19:41770056-41771086	GM10847	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41766631..41773289-chr19:41812153..41817614,9	K562	blood:
2	chr19:41769310..41770884-chr19:41804144..41807027,2	MCF-7	breast:
3	chr19:41703762..41708765-chr19:41768363..41772371,6	MCF-7	breast:
4	chr19:41770026..41770935-chr2:223725702..223726222,2	Hela-S3	cervix:
5	chr19:41766963..41771332-chr19:41813075..41817628,7	K562	blood:
6	chr19:41770083..41771772-chr19:41780839..41782366,2	MCF-7	breast:
7	chr19:41219692..41221966-chr19:41769353..41771568,2	MCF-7	breast:
8	chr19:41769421..41772801-chr19:41806181..41809917,4	MCF-7	breast:
9	chr19:41769787..41771602-chr19:41823393..41825966,2	MCF-7	breast:
10	chr19:41769462..41771518-chr9:139890234..139892822,2	MCF-7	breast:
11	chr14:96968705..96969471-chr19:41770213..41770930,2	Hela-S3	cervix:
12	chr19:41768451..41772660-chr19:41814640..41817683,6	MCF-7	breast:
13	chr19:41767589..41772847-chr19:41812402..41817981,15	MCF-7	breast:
14	chr19:41697323..41700714-chr19:41769063..41770894,3	K562	blood:
15	chr19:41766877..41771286-chr19:41856641..41860631,6	K562	blood:
16	chr19:41723294..41725372-chr19:41769177..41770875,2	MCF-7	breast:

Variant related genes	Relation type
HNRNPUL1	TF binding region
ENSG00000123815	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000167600	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000123983	Chromatin interaction
ENSG00000169583	Chromatin interaction
ENSG00000090060	Chromatin interaction
ENSG00000167601	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10410836	0.96[ASN][1000 genomes]
rs10421990	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11879562	0.95[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11882467	0.82[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs12327659	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12462203	0.95[CHB][hapmap]
rs12974323	0.93[ASN][1000 genomes]
rs12975920	0.95[ASN][1000 genomes]
rs12978323	0.94[ASW][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs12980298	0.92[ASN][1000 genomes]
rs12980480	0.95[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12980839	0.87[ASN][1000 genomes]
rs12983047	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs13345456	0.93[ASN][1000 genomes]
rs16958994	0.90[ASN][1000 genomes]
rs16958996	0.90[ASN][1000 genomes]
rs16958999	0.90[ASN][1000 genomes]
rs1865051	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1865052	0.90[ASN][1000 genomes]
rs1865053	0.95[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2304230	0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2304234	0.88[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.85[ASN][1000 genomes]
rs34075897	0.92[ASN][1000 genomes]
rs34945449	0.87[ASN][1000 genomes]
rs3745295	0.95[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs3752705	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3786555	0.83[ASN][1000 genomes]
rs3816052	0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs3826714	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs4456618	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4802111	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs4802112	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4802113	0.95[CHB][hapmap]
rs4802115	0.84[ASN][1000 genomes]
rs4803448	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs4803449	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs4803451	0.83[ASN][1000 genomes]
rs6508974	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs66724427	0.96[ASN][1000 genomes]
rs67511749	0.90[ASN][1000 genomes]
rs6957	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs7245398	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7246525	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs7248164	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7254679	0.87[ASN][1000 genomes]
rs7256416	0.96[ASN][1000 genomes]
rs7256856	0.94[ASN][1000 genomes]
rs7257310	0.90[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs7257742	0.92[ASN][1000 genomes]
rs7257825	0.95[ASN][1000 genomes]
rs7258749	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs8105161	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs8109167	0.90[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs8109627	0.90[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv17637	chr19:41770228-41815282	Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41767200-41770400	Active TSS	Brain Germinal Matrix	brain
2	chr19:41767400-41772400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:41767600-41770600	Active TSS	Fetal Brain Female	brain
4	chr19:41767600-41771400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr19:41767600-41771400	Active TSS	Fetal Stomach	stomach
6	chr19:41767600-41771800	Active TSS	Right Ventricle	heart
7	chr19:41767600-41772200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr19:41767600-41772200	Active TSS	Psoas Muscle	Psoas
9	chr19:41767600-41772400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr19:41767600-41772400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr19:41767800-41771200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr19:41767800-41771200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:41767800-41771400	Active TSS	Primary T cells from cord blood	blood
14	chr19:41767800-41771400	Active TSS	Brain Angular Gyrus	brain
15	chr19:41767800-41771400	Active TSS	Colon Smooth Muscle	Colon
16	chr19:41767800-41771800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:41767800-41771800	Active TSS	Fetal Kidney	kidney
18	chr19:41767800-41772000	Active TSS	Aorta	Aorta
19	chr19:41767800-41772200	Active TSS	Esophagus	oesophagus
20	chr19:41767800-41772200	Active TSS	Lung	lung
21	chr19:41767800-41772400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr19:41767800-41772400	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr19:41767800-41772400	Active TSS	Right Atrium	heart
24	chr19:41767800-41772600	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr19:41767800-41773200	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr19:41768000-41770400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:41768000-41770400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:41768000-41770400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:41768000-41771200	Active TSS	Colonic Mucosa	Colon
30	chr19:41768000-41771400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:41768000-41771400	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr19:41768000-41771400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr19:41768000-41771600	Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr19:41768000-41771600	Active TSS	Placenta	Placenta
35	chr19:41768000-41771600	Active TSS	Left Ventricle	heart
36	chr19:41768000-41771600	Active TSS	Rectal Smooth Muscle	rectum
37	chr19:41768000-41771600	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr19:41768000-41771800	Active TSS	Fetal Intestine Large	intestine
39	chr19:41768000-41772000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr19:41768000-41772000	Active TSS	Gastric	stomach
41	chr19:41768000-41772200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:41768000-41772200	Active TSS	Ovary	ovary
43	chr19:41768000-41772400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:41768000-41772400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:41768000-41772400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:41768000-41772400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:41768000-41772400	Active TSS	HSMMtube	muscle
48	chr19:41768000-41772600	Active TSS	H9 Cell Line	embryonic stem cell
49	chr19:41768200-41770400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr19:41768200-41770400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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