Variant report

Variant	rs11753645
Chromosome Location	chr6:109695054-109695055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:75)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:75 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MEF2A	chr6:109694633-109695289	GM12878	blood:	n/a	chr6:109694884-109694899
2	MTA3	chr6:109694471-109695493	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:109695011-109695220	Hela-S3	cervix:	n/a	n/a
4	MTA3	chr6:109694816-109695422	GM12878	blood:	n/a	n/a
5	RUNX3	chr6:109694711-109695526	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:109695014-109695230	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:109695021-109695752	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr6:109694964-109695479	GM12892	blood:	n/a	n/a
9	MAZ	chr6:109695046-109695345	GM12878	blood:	n/a	n/a
10	TBL1XR1	chr6:109694770-109695425	GM12878	blood:	n/a	n/a
11	BATF	chr6:109694830-109695425	GM12878	blood:	n/a	n/a
12	ATF2	chr6:109694760-109695330	GM12878	blood:	n/a	n/a
13	STAT5A	chr6:109694969-109695347	GM12878	blood:	n/a	n/a
14	BCLAF1	chr6:109694698-109695758	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:109694965-109695516	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:109685661-109704818	K562	blood:	n/a	n/a
17	EP300	chr6:109694727-109695484	GM12878	blood:	n/a	chr6:109694844-109694857
18	STAT3	chr6:109694866-109695398	GM12878	blood:	n/a	n/a
19	STAT1	chr6:109695028-109695310	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:109694905-109695114	ProgFib	skin:	n/a	n/a
21	POLR2A	chr6:109694462-109696236	GM12878	blood:	n/a	n/a
22	RELA	chr6:109694680-109695500	GM18505	blood:	n/a	n/a
23	PAX5	chr6:109694903-109695248	GM12878	blood:	n/a	n/a
24	SIN3A	chr6:109694927-109695221	GM12878	blood:	n/a	n/a
25	IRF4	chr6:109694874-109695403	GM12878	blood:	n/a	n/a
26	NFYB	chr6:109695001-109695306	GM12878	blood:	n/a	n/a
27	NFIC	chr6:109694698-109695509	GM12878	blood:	n/a	n/a
28	BATF	chr6:109694957-109695339	GM12878	blood:	n/a	n/a
29	SP1	chr6:109694877-109695388	GM12878	blood:	n/a	chr6:109695287-109695301
30	BCLAF1	chr6:109694870-109695427	GM12878	blood:	n/a	n/a
31	NFIC	chr6:109694783-109695410	GM12878	blood:	n/a	n/a
32	POU2F2	chr6:109695006-109695404	GM12891	blood:	n/a	n/a
33	FOXM1	chr6:109694809-109695445	GM12878	blood:	n/a	n/a
34	RCOR1	chr6:109694753-109695376	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:109690802-109696191	HepG2	liver:	n/a	n/a
36	POLR2A	chr6:109694507-109696262	GM12892	blood:	n/a	n/a
37	EP300	chr6:109694985-109695358	GM12878	blood:	n/a	n/a
38	NFATC1	chr6:109694529-109695485	GM12878	blood:	n/a	n/a
39	POLR2A	chr6:109694895-109695428	GM12891	blood:	n/a	n/a
40	POLR2A	chr6:109694977-109695396	GM12891	blood:	n/a	n/a
41	RUNX3	chr6:109694858-109695488	GM12878	blood:	n/a	n/a
42	IRF4	chr6:109694855-109695408	GM12878	blood:	n/a	n/a
43	POLR2A	chr6:109694488-109696198	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:109694893-109695060	MCF-7	breast:	n/a	n/a
45	PAX5	chr6:109694858-109695353	GM12878	blood:	n/a	n/a
46	PAX5	chr6:109694930-109695323	GM12878	blood:	n/a	n/a
47	EBF1	chr6:109694931-109695331	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:109694475-109696323	K562	blood:	n/a	n/a
49	MXI1	chr6:109694740-109695397	GM12878	blood:	n/a	n/a
50	PML	chr6:109694543-109695562	GM12878	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109626057..109628576-chr6:109694970..109697513,2	K562	blood:

No data

Variant related genes	Relation type
CD164	TF binding region
ENSG00000201023	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1048203	0.84[CEU][hapmap]
rs10499052	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs10782162	0.89[CEU][hapmap]
rs11153174	0.81[CEU][hapmap]
rs11153175	0.81[CEU][hapmap]
rs11757877	0.84[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11967108	0.81[CEU][hapmap]
rs12190920	0.80[CEU][hapmap]
rs12197114	0.81[CEU][hapmap]
rs12524502	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12524639	0.81[CEU][hapmap]
rs12528566	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12528712	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12528822	0.84[CEU][hapmap]
rs13192476	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13195517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13199519	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13203252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13220304	0.89[CEU][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs1322818	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1358998	0.84[CEU][hapmap]
rs17070580	0.80[CEU][hapmap]
rs1923725	0.81[CEU][hapmap]
rs2236582	0.84[CEU][hapmap]
rs2275650	0.84[CEU][hapmap]
rs2275652	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34131679	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34292461	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34320275	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35452836	0.84[EUR][1000 genomes]
rs35969918	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3757234	0.81[CEU][hapmap]
rs3757238	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3799835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799840	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4428538	0.83[EUR][1000 genomes]
rs61076041	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61233650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61318425	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67857472	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6929208	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7773095	0.84[CEU][hapmap]
rs9320287	0.80[CEU][hapmap]
rs9480948	0.84[CEU][hapmap]
rs9480957	0.84[CEU][hapmap]
rs9487100	0.81[CEU][hapmap]
rs9885646	0.80[CEU][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11753645	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs11753645	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs11753645	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs11753645	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs11753645	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109675000-109700800	Strong transcription	Placenta	Placenta
2	chr6:109677000-109698200	Strong transcription	Fetal Intestine Large	intestine
3	chr6:109677800-109700600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:109678200-109695200	Strong transcription	Duodenum Mucosa	Duodenum
5	chr6:109678800-109695400	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr6:109678800-109699000	Strong transcription	Dnd41	blood
7	chr6:109679200-109700400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:109679400-109700600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:109680400-109697200	Weak transcription	Fetal Brain Male	brain
10	chr6:109680600-109700600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:109682600-109700800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:109683200-109699800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:109683800-109700600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:109684000-109695400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:109684000-109695800	Weak transcription	Spleen	Spleen
16	chr6:109684000-109702400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:109684200-109695600	Weak transcription	Small Intestine	intestine
18	chr6:109684400-109702400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:109684600-109700200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:109684600-109700400	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr6:109684800-109700200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:109685800-109700600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:109686400-109699000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:109686600-109700200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:109686800-109700200	Strong transcription	HSMM	muscle
26	chr6:109687000-109695800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:109687400-109699200	Strong transcription	HMEC	breast
28	chr6:109687400-109700200	Strong transcription	NH-A	brain
29	chr6:109687600-109700200	Strong transcription	NHEK	skin
30	chr6:109688200-109699400	Strong transcription	HepG2	liver
31	chr6:109689800-109697600	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:109690600-109701800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr6:109691600-109699600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:109692000-109700000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:109692200-109697600	Genic enhancers	Primary hematopoietic stem cells	blood
36	chr6:109692600-109695800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:109692800-109695200	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr6:109692800-109696200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:109692800-109696200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
40	chr6:109692800-109700200	Strong transcription	NHLF	lung
41	chr6:109693000-109695200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:109693000-109699200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:109693000-109699600	Strong transcription	Fetal Kidney	kidney
44	chr6:109693200-109696200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr6:109693200-109696200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
46	chr6:109693200-109696200	Genic enhancers	K562	blood
47	chr6:109693200-109696200	Genic enhancers	Monocytes-CD14+_RO01746	blood
48	chr6:109693200-109696400	Genic enhancers	Primary T cells from cord blood	blood
49	chr6:109693200-109698200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:109693200-109699200	Genic enhancers	Primary T helper cells PMA-I stimulated	--

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