Variant report

Variant	rs901823
Chromosome Location	chr11:68205578-68205579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr11:68204451-68205624	K562	blood:	n/a	chr11:68205044-68205054 chr11:68205043-68205055 chr11:68205045-68205053 chr11:68205046-68205053 chr11:68205045-68205054
2	JUND	chr11:68204681-68205593	SK-N-SH	brain:	n/a	chr11:68205044-68205054 chr11:68205043-68205055 chr11:68205045-68205053 chr11:68205046-68205053 chr11:68205045-68205054

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:68205561-68205611	NB4	blood:	n/a
2	chr11:68205561-68205611	AoSMC	blood vessel:	n/a
3	chr11:68205561-68205611	A549	lung:	n/a
4	chr11:68205561-68205611	ProgFib	skin:	n/a
5	chr11:68205561-68205611	U87	brain:	n/a
6	chr11:68205561-68205611	AG04450	lung:	fetal
7	chr11:68205561-68205611	K562	blood:	n/a
8	chr11:68205561-68205611	GM12891	blood:	n/a
9	chr11:68205561-68205611	T-47D	breast:	n/a
10	chr11:68205561-68205611	NH-A	brain:	n/a
11	chr11:68205561-68205611	LNCaP	prostate:	n/a
12	chr11:68205561-68205611	BJ	skin:	n/a
13	chr11:68205561-68205611	AG04449	skin:	fetal
14	chr11:68205561-68205611	H1-hESC	embryonic stem cell:	embryo
15	chr11:68205561-68205611	BE2_C	brain:	n/a
16	chr11:68205561-68205611	AG10803	skin:	n/a
17	chr11:68205561-68205611	HMEC	breast:	n/a
18	chr11:68205561-68205611	HepG2	liver:	n/a
19	chr11:68205561-68205611	RPTEC	kidney:	n/a
20	chr11:68205561-68205611	SK-N-MC	brain:	n/a
21	chr11:68205561-68205611	GM06990	blood:	n/a
22	chr11:68205561-68205611	MCF10A-Er-Src	breast:	n/a
23	chr11:68205561-68205611	Caco-2	colon:	n/a
24	chr11:68205561-68205611	HCPEpiC	choroid plexus:	n/a
25	chr11:68205561-68205611	CMK	blood:	n/a
26	chr11:68205561-68205611	HRE	kidney:	n/a
27	chr11:68205561-68205611	GM12878	blood:	n/a
28	chr11:68205561-68205611	NHBE	bronchial:	n/a
29	chr11:68205561-68205611	NHDF-neo	bronchial:	n/a
30	chr11:68205561-68205611	Hela-S3	cervix:	n/a
31	chr11:68205561-68205611	ovcar-3	ovarian:	n/a
32	chr11:68205561-68205611	MCF-7	breast:	n/a
33	chr11:68205561-68205611	HNPCEpiC	eye:	n/a
34	chr11:68205561-68205611	SAEC	small airway:	n/a
35	chr11:68205561-68205611	HEEpiC	esophagus:	n/a
36	chr11:68205561-68205611	GM19239	blood:	n/a
37	chr11:68205561-68205611	GM12892	blood:	n/a
38	chr11:68205561-68205611	HCT-116	colon:	n/a
39	chr11:68205561-68205611	HCF	heart:	n/a
40	chr11:68205561-68205611	SK-N-SH	brain:	n/a
41	chr11:68205561-68205611	HUVEC	blood vessel:	n/a
42	chr11:68205561-68205611	PrEC	prostate:	n/a
43	chr11:68205561-68205611	HL-60	blood:	n/a
44	chr11:68205561-68205611	IMR90	lung:	fetal
45	chr11:68205561-68205611	HCM	heart:	n/a
46	chr11:68205561-68205611	Hepatocyte	liver:	n/a
47	chr11:68205561-68205611	AG09319	gingival:	n/a
48	chr11:68205561-68205611	HIPEpiC	eye:	n/a
49	chr11:68205561-68205611	AG09309	skin:	n/a
50	chr11:68205561-68205611	HAEpiC	amniotic membrane:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:68038613..68041081-chr11:68205366..68206871,2	K562	blood:
2	chr11:68198542..68202152-chr11:68203500..68206057,4	K562	blood:
3	chr11:68037835..68039908-chr11:68205347..68207124,2	MCF-7	breast:
4	chr11:68199257..68202152-chr11:68202690..68206057,4	K562	blood:
5	chr11:68204961..68210848-chr11:68212670..68216087,6	K562	blood:

No data

Variant related genes	Relation type
LRP5	TF binding region
LRP5	CpG island
ENSG00000171067	Chromatin interaction
ENSG00000162337	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10501398	0.90[MEX][hapmap]
rs11228295	0.85[MEX][hapmap]
rs11822059	0.90[MEX][hapmap]
rs1785493	0.80[EUR][1000 genomes]
rs23691	0.86[EUR][1000 genomes]
rs2472415	0.85[CHB][hapmap]
rs2840367	0.90[MEX][hapmap]
rs314750	0.85[CEU][hapmap];0.85[CHB][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs314751	0.86[EUR][1000 genomes]
rs3740628	0.90[MEX][hapmap]
rs3853616	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs471966	0.87[EUR][1000 genomes]
rs497261	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs525592	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs531163	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs546803	0.85[CHB][hapmap]
rs554734	0.95[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs556442	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs576118	0.85[CHB][hapmap]
rs583545	0.85[CHB][hapmap]
rs599083	0.95[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs599301	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603129	0.84[EUR][1000 genomes]
rs607887	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs608343	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs624003	0.90[MEX][hapmap]
rs630225	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs638076	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs640569	0.85[CHB][hapmap]
rs653056	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs667126	0.85[CHB][hapmap]
rs683978	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs689075	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7108376	0.90[MEX][hapmap]
rs7119422	0.90[MEX][hapmap]
rs7126451	0.90[MEX][hapmap]
rs7950129	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347272	chr11:67969427-68218997	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
2	nsv897857	chr11:68056770-68231240	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897858	chr11:68077238-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv897859	chr11:68102000-68231240	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv897860	chr11:68102000-68293545	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1047532	chr11:68103330-68239242	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv541082	chr11:68103330-68239242	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1039671	chr11:68120571-68206630	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1036561	chr11:68123135-68315685	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv897862	chr11:68129606-68236389	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv469965	chr11:68140781-68217420	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv555285	chr11:68144283-68231240	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv468618	chr11:68171013-68231240	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv897863	chr11:68186392-68251460	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv555286	chr11:68192346-68207287	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv520841	chr11:68199008-68217420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	esv1792339	chr11:68199008-68299226	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	esv1803199	chr11:68199008-68299226	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	esv1842405	chr11:68199008-68299226	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv526402	chr11:68201295-68217420	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs901823	RBM4B	cis	cerebellum	SCAN
rs901823	SAPS3	cis	multi-tissue	Pritchard
rs901823	CARNS1	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68176000-68210400	Strong transcription	HepG2	liver
2	chr11:68182800-68222200	Weak transcription	Small Intestine	intestine
3	chr11:68197400-68207600	Weak transcription	Primary B cells from cord blood	blood
4	chr11:68197400-68208000	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:68197400-68208800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:68197400-68210600	Strong transcription	Dnd41	blood
7	chr11:68197400-68214400	Strong transcription	Fetal Intestine Small	intestine
8	chr11:68197400-68214600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:68197400-68214800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:68197400-68216400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr11:68197400-68217800	Strong transcription	Liver	Liver
12	chr11:68197600-68206200	Weak transcription	Fetal Kidney	kidney
13	chr11:68197600-68207000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr11:68197600-68207400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:68197600-68207600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:68197600-68208400	Strong transcription	Fetal Brain Female	brain
17	chr11:68197600-68210800	Strong transcription	Brain Germinal Matrix	brain
18	chr11:68197600-68217800	Strong transcription	Fetal Intestine Large	intestine
19	chr11:68197600-68227000	Weak transcription	Brain Hippocampus Middle	brain
20	chr11:68197800-68206400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:68197800-68206600	Strong transcription	Ovary	ovary
22	chr11:68197800-68207000	Strong transcription	Aorta	Aorta
23	chr11:68197800-68208000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:68197800-68208800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:68198200-68209600	Strong transcription	Esophagus	oesophagus
26	chr11:68198200-68210600	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:68198400-68208400	Strong transcription	Thymus	Thymus
28	chr11:68198400-68208800	Weak transcription	GM12878-XiMat	blood
29	chr11:68198600-68206200	Weak transcription	Brain Substantia Nigra	brain
30	chr11:68198600-68209200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:68198600-68209400	Weak transcription	Brain Angular Gyrus	brain
32	chr11:68198600-68215000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:68198800-68227000	Weak transcription	Brain Anterior Caudate	brain
34	chr11:68199400-68207200	Strong transcription	Colon Smooth Muscle	Colon
35	chr11:68199600-68210600	Strong transcription	Colonic Mucosa	Colon
36	chr11:68200000-68207000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr11:68200200-68207200	Strong transcription	Fetal Thymus	thymus
38	chr11:68200600-68210200	Strong transcription	Primary T cells from cord blood	blood
39	chr11:68201000-68227400	Weak transcription	Fetal Brain Male	brain
40	chr11:68201600-68207600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:68201600-68209400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr11:68201600-68218800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:68201800-68206600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:68203000-68206200	Weak transcription	Fetal Lung	lung
45	chr11:68203200-68207400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:68203400-68205600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr11:68203800-68205600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:68203800-68205600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:68203800-68205800	Enhancers	Left Ventricle	heart
50	chr11:68203800-68206000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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