Variant report

Variant	rs11229864
Chromosome Location	chr11:58938892-58938893
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	RAD21	chr11:58938811-58939703	A549	lung:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939507-58939521 chr11:58939065-58939079 chr11:58939069-58939079
2	NFATC1	chr11:58938785-58939830	GM12878	blood:	n/a	n/a
3	RAD21	chr11:58938812-58939690	Hela-S3	cervix:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939507-58939521 chr11:58939065-58939079 chr11:58939069-58939079
4	MTA3	chr11:58938544-58939888	GM12878	blood:	n/a	n/a
5	POU2F2	chr11:58938873-58941108	GM12878	blood:	n/a	chr11:58940304-58940316 chr11:58939780-58939798 chr11:58939563-58939575 chr11:58940301-58940313 chr11:58939785-58939792 chr11:58939784-58939794 chr11:58939104-58939116 chr11:58939784-58939793
6	RAD21	chr11:58938727-58939747	IMR90	lung:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939507-58939521 chr11:58939065-58939079 chr11:58939069-58939079
7	CTCF	chr11:58938362-58940223	SK-N-SH	brain:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939508-58939521 chr11:58939068-58939078
8	POLR2A	chr11:58938795-58945281	GM12878	blood:	n/a	n/a
9	CUX1	chr11:58938854-58939567	GM12878	blood:	n/a	n/a
10	SMC3	chr11:58938856-58939661	HepG2	liver:	n/a	chr11:58939069-58939079 chr11:58939103-58939117 chr11:58939065-58939079
11	MAX	chr11:58938768-58940390	A549	lung:	n/a	chr11:58939511-58939521
12	SP1	chr11:58938841-58939717	A549	lung:	n/a	chr11:58939110-58939120 chr11:58939581-58939593 chr11:58939582-58939591 chr11:58939110-58939120
13	MAX	chr11:58938887-58939779	NB4	blood:	n/a	chr11:58939511-58939521
14	TCF12	chr11:58938800-58939777	A549	lung:	n/a	chr11:58939063-58939073
15	CTCF	chr11:58938809-58939263	K562	blood:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939068-58939078
16	ZNF143	chr11:58938874-58939764	K562	blood:	n/a	chr11:58939440-58939450
17	NRF1	chr11:58938864-58939279	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr11:58938854-58939885	GM12892	blood:	n/a	n/a
19	POLR2A	chr11:58938860-58941234	GM12892	blood:	n/a	n/a
20	MAZ	chr11:58938731-58942643	IMR90	lung:	n/a	chr11:58939511-58939521 chr11:58942531-58942541
21	RAD21	chr11:58938700-58939692	A549	lung:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939507-58939521 chr11:58939065-58939079 chr11:58939069-58939079
22	ZC3H11A	chr11:58938877-58939700	K562	blood:	n/a	n/a
23	KAP1	chr11:58938821-58939655	HEK293	kidney:	n/a	n/a
24	RUNX3	chr11:58938852-58939825	GM12878	blood:	n/a	n/a
25	CTCF	chr11:58938845-58939735	GM12878	blood:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939508-58939521 chr11:58939068-58939078
26	YY1	chr11:58938888-58940427	GM12892	blood:	n/a	chr11:58940048-58940059
27	MXI1	chr11:58938839-58939800	GM12878	blood:	n/a	n/a
28	RCOR1	chr11:58938861-58939777	HepG2	liver:	n/a	n/a
29	RAD21	chr11:58938880-58939742	H1-hESC	embryonic stem cell:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939507-58939521 chr11:58939065-58939079 chr11:58939069-58939079
30	CTCF	chr11:58938864-58939709	H1-hESC	embryonic stem cell:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939508-58939521 chr11:58939068-58939078
31	ATF2	chr11:58938888-58939552	H1-hESC	embryonic stem cell:	n/a	n/a
32	ZNF143	chr11:58938880-58939713	GM12878	blood:	n/a	chr11:58939440-58939450
33	BCLAF1	chr11:58938681-58939885	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:58938836-58941358	H1-neurons	neurons:	n/a	n/a
35	CTCF	chr11:58938856-58939708	K562	blood:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939508-58939521 chr11:58939068-58939078
36	MAX	chr11:58938784-58939932	HCT-116	colon:	n/a	chr11:58939511-58939521
37	CHD2	chr11:58938891-58939837	GM12878	blood:	n/a	n/a
38	CTCF	chr11:58938889-58939231	SK-N-SH_RA	brain:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939068-58939078
39	CTCF	chr11:58938811-58939769	MCF-7	breast:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939508-58939521 chr11:58939068-58939078
40	POU2F2	chr11:58938870-58939252	GM12891	blood:	n/a	chr11:58939104-58939116
41	MAFK	chr11:58938880-58939625	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr11:58938729-58939868	HCT-116	colon:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939508-58939521 chr11:58939068-58939078
43	CTCF	chr11:58938880-58939214	HUVEC	blood vessel:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939068-58939078
44	BHLHE40	chr11:58938875-58939776	GM12878	blood:	n/a	n/a
45	MXI1	chr11:58938770-58940352	IMR90	lung:	n/a	n/a
46	CTCF	chr11:58938835-58939294	A549	lung:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939068-58939078
47	RAD21	chr11:58938657-58939754	SK-N-SH	brain:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939507-58939521 chr11:58939065-58939079 chr11:58939069-58939079
48	MAX	chr11:58938889-58939853	H1-hESC	embryonic stem cell:	n/a	chr11:58939511-58939521
49	BCLAF1	chr11:58938831-58939880	GM12878	blood:	n/a	n/a
50	RAD21	chr11:58938839-58939229	SK-N-SH_RA	brain:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939065-58939079 chr11:58939069-58939079

No.	Distal block	Cell Line	Cell type
1	chr11:58937186..58939247-chr11:58980596..58982199,2	K562	blood:
2	chr11:58938664..58939165-chr11:59051489..59052229,2	K562	blood:
3	chr11:58343237..58345881-chr11:58936566..58939542,2	K562	blood:
4	chr11:58911158..58913877-chr11:58937423..58939058,2	K562	blood:

Variant related genes	Relation type
DTX4	TF binding region
ENSG00000166801	Chromatin interaction
ENSG00000263999	Chromatin interaction
ENSG00000214797	Chromatin interaction
ENSG00000110031	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10792220	0.82[CHB][hapmap]
rs10896919	0.94[CHB][hapmap]
rs10896920	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs12280905	0.94[CHB][hapmap]
rs1938590	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs2845559	0.94[CHB][hapmap]
rs4287350	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs4382926	0.94[CHB][hapmap]
rs592110	0.94[CHB][hapmap]
rs610764	0.88[CHB][hapmap]
rs7939969	0.94[CHB][hapmap];0.81[CHD][hapmap]

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	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3427190	chr11:58938601-58941149	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv3399192	chr11:58938776-58941074	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11229864	CCDC86	cis	parietal	SCAN
rs11229864	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs11229864	SNORA57	cis	parietal	SCAN
rs11229864	MPEG1	Cis_1M	lymphoblastoid	RTeQTL
rs11229864	SLC15A3	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58934800-58939000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:58937600-58939000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:58937600-58939000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:58937800-58939000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:58938200-58939000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:58938200-58939000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr11:58938200-58939000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:58938600-58939200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:58938600-58942000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:58938800-58939000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr11:58938800-58939000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:58938800-58939000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:58938800-58939000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr11:58938800-58939000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr11:58938800-58939000	Enhancers	Primary B cells from cord blood	blood
16	chr11:58938800-58939000	Enhancers	Primary B cells from peripheral blood	blood
17	chr11:58938800-58939000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr11:58938800-58939000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr11:58938800-58939000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:58938800-58939000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr11:58938800-58939000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:58938800-58939000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr11:58938800-58939000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:58938800-58939000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr11:58938800-58939000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr11:58938800-58939000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:58938800-58939000	Enhancers	Liver	Liver
28	chr11:58938800-58939000	Enhancers	Duodenum Mucosa	Duodenum
29	chr11:58938800-58939000	Enhancers	Fetal Kidney	kidney
30	chr11:58938800-58939000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr11:58938800-58939000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
32	chr11:58938800-58939000	Bivalent Enhancer	A549	lung
33	chr11:58938800-58939000	Flanking Bivalent TSS/Enh	Dnd41	blood
34	chr11:58938800-58939000	Flanking Active TSS	GM12878-XiMat	blood
35	chr11:58938800-58939000	Enhancers	Hela-S3	cervix
36	chr11:58938800-58939000	Enhancers	HMEC	breast
37	chr11:58938800-58939000	Enhancers	NHEK	skin
38	chr11:58938800-58939200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr11:58938800-58939200	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr11:58938800-58939400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr11:58938800-58939400	Enhancers	Fetal Brain Male	brain
42	chr11:58938800-58939800	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr11:58938800-58939800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:58938800-58940200	Active TSS	H1 Cell Line	embryonic stem cell
45	chr11:58938800-58940200	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr11:58938800-58940200	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr11:58938800-58940200	Active TSS	Primary T cells from cord blood	blood
48	chr11:58938800-58940200	Active TSS	Brain Angular Gyrus	brain
49	chr11:58938800-58940200	Active TSS	Brain Germinal Matrix	brain
50	chr11:58938800-58940200	Active TSS	Fetal Brain Female	brain

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