Variant report

Variant	rs1946613
Chromosome Location	chr19:41767785-41767786
allele	A/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	RAD21	chr19:41767758-41768738	HCT-116	colon:	n/a	n/a
2	USF1	chr19:41767783-41768701	HCT-116	colon:	n/a	n/a
3	POLR2A	chr19:41767388-41771764	U87	brain:	n/a	n/a
4	TCF12	chr19:41767768-41768726	A549	lung:	n/a	n/a
5	POLR2A	chr19:41767678-41771748	Hela-S3	cervix:	n/a	n/a
6	MAZ	chr19:41767177-41772220	IMR90	lung:	n/a	chr19:41768441-41768450 chr19:41768481-41768490 chr19:41771759-41771769 chr19:41768482-41768493 chr19:41770252-41770262
7	USF1	chr19:41767778-41768727	A549	lung:	n/a	n/a
8	GATA3	chr19:41767680-41771473	A549	lung:	n/a	chr19:41769052-41769060 chr19:41769485-41769493 chr19:41769049-41769062
9	TCF12	chr19:41767598-41772879	A549	lung:	n/a	chr19:41771163-41771170
10	ATF3	chr19:41767707-41768748	A549	lung:	n/a	n/a
11	RAD21	chr19:41767753-41768699	A549	lung:	n/a	n/a
12	POLR2A	chr19:41767392-41771263	SK-N-SH	brain:	n/a	n/a
13	SIN3AK20	chr19:41767289-41770705	A549	lung:	n/a	n/a
14	POLR2A	chr19:41767659-41768745	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr19:41766822-41772154	IMR90	lung:	n/a	n/a
16	POLR2A	chr19:41767576-41768812	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr19:41766581-41772173	U87	brain:	n/a	n/a
18	BCL3	chr19:41767315-41771247	A549	lung:	n/a	chr19:41770820-41770833 chr19:41769404-41769417 chr19:41770075-41770084 chr19:41768447-41768460 chr19:41770716-41770725
19	PBX3	chr19:41767666-41768748	SK-N-SH	brain:	n/a	n/a
20	FOSL2	chr19:41767461-41772092	A549	lung:	n/a	chr19:41770714-41770723 chr19:41769880-41769889 chr19:41769949-41769961 chr19:41770306-41770315 chr19:41770166-41770175 chr19:41769082-41769093 chr19:41768151-41768159
21	MXI1	chr19:41767723-41772046	SK-N-SH	brain:	n/a	chr19:41770147-41770162
22	CTCF	chr19:41767590-41768737	SK-N-SH	brain:	n/a	chr19:41768327-41768345 chr19:41768328-41768344
23	CTCF	chr19:41766421-41772168	A549	lung:	n/a	chr19:41768327-41768345 chr19:41769790-41769803 chr19:41768328-41768344
24	POLR2A	chr19:41767199-41771324	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr19:41767679-41768707	HCT-116	colon:	n/a	n/a
26	SP1	chr19:41767683-41771936	A549	lung:	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 chr19:41768450-41768461 chr19:41769814-41769835 chr19:41770716-41770725 chr19:41770902-41770915 chr19:41768450-41768462 chr19:41768451-41768461 chr19:41770907-41770917 chr19:41768452-41768461 chr19:41769745-41769754 chr19:41768447-41768461 chr19:41770907-41770916 chr19:41770050-41770062 chr19:41770714-41770726 chr19:41768451-41768460 chr19:41768452-41768461 chr19:41770715-41770724 chr19:41768450-41768462 chr19:41770906-41770918
27	BCL3	chr19:41767350-41772062	A549	lung:	n/a	chr19:41770820-41770833 chr19:41769404-41769417 chr19:41770075-41770084 chr19:41768447-41768460 chr19:41770716-41770725 chr19:41771949-41771957
28	PBX3	chr19:41767630-41768741	A549	lung:	n/a	n/a
29	RAD21	chr19:41767753-41768733	HCT-116	colon:	n/a	n/a
30	REST	chr19:41767571-41772057	A549	lung:	n/a	chr19:41768350-41768368 chr19:41771946-41771956 chr19:41770353-41770362 chr19:41771916-41771929 chr19:41768349-41768369
31	ETS1	chr19:41767671-41768580	A549	lung:	n/a	chr19:41768431-41768438
32	GABPA	chr19:41767708-41768684	A549	lung:	n/a	n/a
33	SMC3	chr19:41767322-41769641	SK-N-SH	brain:	n/a	n/a
34	REST	chr19:41767706-41771869	H1-neurons	neurons:	n/a	chr19:41768350-41768368 chr19:41770353-41770362 chr19:41768349-41768369
35	SP1	chr19:41767718-41771821	A549	lung:	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 chr19:41768450-41768461 chr19:41769814-41769835 chr19:41770716-41770725 chr19:41770902-41770915 chr19:41768450-41768462 chr19:41768451-41768461 chr19:41770907-41770917 chr19:41768452-41768461 chr19:41769745-41769754 chr19:41768447-41768461 chr19:41770907-41770916 chr19:41770050-41770062 chr19:41770714-41770726 chr19:41768451-41768460 chr19:41768452-41768461 chr19:41770715-41770724 chr19:41768450-41768462 chr19:41770906-41770918
36	MAX	chr19:41767632-41772165	A549	lung:	n/a	chr19:41768441-41768450 chr19:41768481-41768490 chr19:41771759-41771769 chr19:41768482-41768493 chr19:41770252-41770262
37	POLR2A	chr19:41767388-41772018	U87	brain:	n/a	n/a
38	EP300	chr19:41767698-41768789	A549	lung:	n/a	n/a
39	SIN3AK20	chr19:41767782-41768754	A549	lung:	n/a	n/a
40	POLR2A	chr19:41766581-41772179	U87	brain:	n/a	n/a
41	ETS1	chr19:41767741-41768724	A549	lung:	n/a	chr19:41768431-41768438
42	RAD21	chr19:41767684-41768821	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr19:41767258-41772108	HUVEC	blood vessel:	n/a	n/a
44	CHD1	chr19:41767372-41774470	IMR90	lung:	n/a	chr19:41770254-41770264 chr19:41768452-41768462
45	POLR2A	chr19:41767679-41768704	HCT-116	colon:	n/a	n/a
46	MXI1	chr19:41767754-41768695	IMR90	lung:	n/a	n/a
47	MAX	chr19:41767728-41768743	A549	lung:	n/a	chr19:41768441-41768450 chr19:41768481-41768490 chr19:41768482-41768493
48	SIX5	chr19:41767546-41771579	A549	lung:	n/a	chr19:41769869-41769878
49	MAX	chr19:41767701-41768763	HCT-116	colon:	n/a	chr19:41768441-41768450 chr19:41768481-41768490 chr19:41768482-41768493
50	POLR2A	chr19:41767388-41772037	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41753148..41755079-chr19:41765835..41768228,2	MCF-7	breast:
2	chr19:41698019..41700083-chr19:41767122..41769558,2	K562	blood:
3	chr19:41766631..41773289-chr19:41812153..41817614,9	K562	blood:
4	chr19:41766963..41771332-chr19:41813075..41817628,7	K562	blood:
5	chr19:41254948..41257942-chr19:41767479..41769277,2	MCF-7	breast:
6	chr19:41723453..41725082-chr19:41766152..41768338,2	MCF-7	breast:
7	chr19:41767589..41772847-chr19:41812402..41817981,15	MCF-7	breast:
8	chr19:41766877..41771286-chr19:41856641..41860631,6	K562	blood:
9	chr19:41698985..41702051-chr19:41767021..41770015,3	MCF-7	breast:
10	chr19:41729266..41732729-chr19:41766701..41770009,7	K562	blood:
11	chr19:41767651..41769904-chr19:41902855..41905283,2	K562	blood:

Variant related genes	Relation type
HNRNPUL1	TF binding region
ENSG00000167600	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000077348	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000167601	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10410836	0.84[EUR][1000 genomes]
rs10421990	0.84[EUR][1000 genomes]
rs1056854	0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs11466345	0.80[JPT][hapmap]
rs11466347	0.83[ASN][1000 genomes]
rs11466359	0.83[ASN][1000 genomes]
rs11879429	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11879435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11879562	0.84[EUR][1000 genomes]
rs11880564	0.88[ASN][1000 genomes]
rs11880729	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11881940	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11881953	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12327659	0.84[EUR][1000 genomes]
rs12972266	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12972779	0.85[ASN][1000 genomes]
rs12972949	0.98[ASN][1000 genomes]
rs12974323	0.84[EUR][1000 genomes]
rs12974420	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12976536	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12977563	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12978323	0.84[CHB][hapmap]
rs12980267	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12980480	0.84[EUR][1000 genomes]
rs12980942	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12981053	0.90[ASN][1000 genomes]
rs12982872	0.84[ASN][1000 genomes]
rs12983027	0.86[ASN][1000 genomes]
rs12983339	0.97[ASN][1000 genomes]
rs12984160	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12985162	0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12985339	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1946612	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2053086	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241718	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2241719	0.88[ASN][1000 genomes]
rs2241720	0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2304230	0.84[EUR][1000 genomes]
rs2304231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304235	0.84[ASN][1000 genomes]
rs34322801	0.88[ASN][1000 genomes]
rs34772093	0.90[ASN][1000 genomes]
rs35310790	0.84[ASN][1000 genomes]
rs35501756	0.88[ASN][1000 genomes]
rs35546772	0.91[ASN][1000 genomes]
rs35812313	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3745295	0.84[EUR][1000 genomes]
rs3752705	0.84[EUR][1000 genomes]
rs3760659	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs3760660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786556	0.84[ASN][1000 genomes]
rs3816052	0.84[EUR][1000 genomes]
rs4591267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61459202	0.90[ASN][1000 genomes]
rs66724427	0.84[EUR][1000 genomes]
rs67744888	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248164	0.84[EUR][1000 genomes]
rs7250883	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7256416	0.84[EUR][1000 genomes]
rs7256856	0.84[EUR][1000 genomes]
rs7256873	0.83[ASN][1000 genomes]
rs7257825	0.84[EUR][1000 genomes]
rs7258749	0.84[EUR][1000 genomes]
rs8103839	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8105901	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41732600-41768800	Weak transcription	Small Intestine	intestine
2	chr19:41736400-41767800	Strong transcription	Placenta Amnion	Placenta Amnion
3	chr19:41736600-41767800	Weak transcription	Brain Angular Gyrus	brain
4	chr19:41755000-41767800	Weak transcription	Hela-S3	cervix
5	chr19:41755000-41768000	Weak transcription	Gastric	stomach
6	chr19:41757400-41767800	Weak transcription	Right Atrium	heart
7	chr19:41758600-41768000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:41764000-41767800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr19:41764200-41767800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr19:41764200-41767800	Weak transcription	Brain Substantia Nigra	brain
11	chr19:41764200-41768400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr19:41764400-41769000	Weak transcription	Spleen	Spleen
13	chr19:41765200-41767800	Weak transcription	Fetal Kidney	kidney
14	chr19:41765400-41767800	Weak transcription	Brain Anterior Caudate	brain
15	chr19:41765800-41767800	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:41765800-41767800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:41766000-41767800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:41766000-41767800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:41766000-41767800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr19:41766000-41767800	Weak transcription	Aorta	Aorta
21	chr19:41766000-41767800	Weak transcription	Fetal Intestine Large	intestine
22	chr19:41766000-41767800	Weak transcription	Fetal Lung	lung
23	chr19:41766000-41768000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:41766000-41768000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr19:41766000-41768000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:41766000-41768000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:41766000-41768000	Weak transcription	Placenta	Placenta
28	chr19:41766000-41768000	Weak transcription	Left Ventricle	heart
29	chr19:41766000-41768000	Weak transcription	Ovary	ovary
30	chr19:41766200-41767800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:41766600-41767800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr19:41766600-41767800	Weak transcription	Fetal Intestine Small	intestine
33	chr19:41767000-41767800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr19:41767200-41767800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:41767200-41767800	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr19:41767200-41767800	Genic enhancers	Osteobl	bone
37	chr19:41767200-41768000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:41767200-41768200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:41767200-41768200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:41767200-41770400	Active TSS	Brain Germinal Matrix	brain
41	chr19:41767400-41767800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:41767400-41767800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr19:41767400-41767800	Enhancers	Primary T cells fromperipheralblood	blood
44	chr19:41767400-41767800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr19:41767400-41767800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:41767400-41767800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:41767400-41767800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:41767400-41767800	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr19:41767400-41767800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr19:41767400-41767800	Enhancers	Fetal Brain Male	brain

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