Variant report

Variant	rs1130199
Chromosome Location	chr17:38447569-38447570
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	POLR2A	chr17:38446493-38447933	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr17:38447420-38447570	SAEC	small airway:	n/a	n/a
3	POLR2A	chr17:38447533-38447908	K562	blood:	n/a	n/a
4	POLR2A	chr17:38446631-38447851	HepG2	liver:	n/a	n/a
5	CTCF	chr17:38446552-38447763	A549	lung:	n/a	chr17:38447146-38447156 chr17:38447143-38447161 chr17:38447138-38447159 chr17:38447144-38447160
6	RAD21	chr17:38446758-38447900	SK-N-SH	brain:	n/a	chr17:38447141-38447160 chr17:38447143-38447155 chr17:38447144-38447157
7	YY1	chr17:38447460-38447737	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:38447498-38447826	K562	blood:	n/a	n/a
9	POLR2A	chr17:38447554-38447914	K562	blood:	n/a	n/a
10	CTCF	chr17:38446452-38447912	SK-N-SH	brain:	n/a	chr17:38447146-38447156 chr17:38447143-38447161 chr17:38447138-38447159 chr17:38447144-38447160
11	POLR2A	chr17:38447481-38448001	GM12892	blood:	n/a	n/a
12	POLR2A	chr17:38446766-38447933	K562	blood:	n/a	n/a
13	BATF	chr17:38447424-38447813	GM12878	blood:	n/a	n/a
14	SMC3	chr17:38446673-38447829	SK-N-SH	brain:	n/a	chr17:38447145-38447159
15	MXI1	chr17:38447473-38447660	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr17:38447510-38447895	PFSK-1	brain:	n/a	n/a
17	CTCF	chr17:38447540-38447690	AG10803	skin:	n/a	n/a
18	BATF	chr17:38447457-38447758	GM12878	blood:	n/a	n/a
19	POLR2A	chr17:38447432-38447875	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr17:38447536-38447761	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr17:38447440-38447590	HEEpiC	esophagus:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38447313..38449363-chr17:38472894..38474903,2	K562	blood:
2	chr17:38170093..38171095-chr17:38447011..38447683,3	K562	blood:
3	chr17:38373931..38375923-chr17:38445660..38448267,2	K562	blood:
4	chr17:38269331..38269965-chr17:38446655..38447580,2	K562	blood:
5	chr17:38357895..38358717-chr17:38446973..38447634,3	MCF-7	breast:
6	chr17:38444029..38445656-chr17:38445740..38447882,2	MCF-7	breast:

Variant related genes	Relation type
CDC6	TF binding region
ENSG00000265799	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000171475	Chromatin interaction
ENSG00000094804	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12936565	0.92[ASW][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs12937995	0.92[ASW][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12944531	0.85[AFR][1000 genomes]
rs12947188	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34789145	0.92[ASW][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7213066	0.86[AFR][1000 genomes]
rs7218938	0.83[YRI][hapmap];0.90[AMR][1000 genomes]
rs7224658	0.92[ASW][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs8065665	0.92[ASW][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs8066144	0.81[LWK][hapmap];0.83[MKK][hapmap]
rs8067148	0.82[AFR][1000 genomes]
rs8072718	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs8074251	0.83[AFR][1000 genomes]
rs8076915	0.92[ASW][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs9892367	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1130199	RAPGEFL1	cis	multi-tissue	Pritchard
rs1130199	RAPGEFL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38444600-38451600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:38444600-38454600	Weak transcription	Ovary	ovary
3	chr17:38444600-38459400	Weak transcription	Brain Angular Gyrus	brain
4	chr17:38444600-38459400	Weak transcription	Spleen	Spleen
5	chr17:38444600-38459600	Weak transcription	Brain Anterior Caudate	brain
6	chr17:38444600-38459600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr17:38444600-38459600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr17:38444800-38449400	Weak transcription	Adipose Nuclei	Adipose
9	chr17:38444800-38451800	Weak transcription	Fetal Brain Female	brain
10	chr17:38444800-38459200	Weak transcription	Fetal Intestine Large	intestine
11	chr17:38444800-38459400	Weak transcription	Fetal Kidney	kidney
12	chr17:38444800-38459400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr17:38444800-38459600	Weak transcription	Right Ventricle	heart
14	chr17:38444800-38459600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr17:38444800-38462600	Weak transcription	Esophagus	oesophagus
16	chr17:38445000-38452000	Weak transcription	Fetal Intestine Small	intestine
17	chr17:38445000-38459600	Weak transcription	Colonic Mucosa	Colon
18	chr17:38445200-38447800	Transcr. at gene 5' and 3'	Dnd41	blood
19	chr17:38445400-38447600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:38445400-38447600	Weak transcription	Fetal Muscle Leg	muscle
21	chr17:38445400-38447800	Transcr. at gene 5' and 3'	Hela-S3	cervix
22	chr17:38445400-38449400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr17:38445400-38451800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr17:38445400-38452000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr17:38445400-38459400	Weak transcription	Primary T cells from cord blood	blood
26	chr17:38445400-38459400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:38445600-38447600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:38445600-38449600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr17:38445600-38449600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr17:38445600-38449800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr17:38445600-38449800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr17:38445600-38450000	Strong transcription	Fetal Stomach	stomach
33	chr17:38445600-38457400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr17:38445600-38459600	Weak transcription	Primary B cells from cord blood	blood
35	chr17:38445600-38460200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:38445600-38462600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr17:38445800-38447800	Genic enhancers	K562	blood
38	chr17:38445800-38448000	Genic enhancers	HepG2	liver
39	chr17:38445800-38449000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:38445800-38449600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr17:38445800-38449800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr17:38445800-38451600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr17:38445800-38457200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr17:38446000-38447600	Weak transcription	Thymus	Thymus
45	chr17:38446000-38449800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr17:38446000-38451800	Weak transcription	Brain Germinal Matrix	brain
47	chr17:38446000-38452400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr17:38446000-38459400	Strong transcription	Fetal Thymus	thymus
49	chr17:38446000-38461000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:38446200-38450800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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