Variant report

Variant	rs11098994
Chromosome Location	chr4:129888651-129888652
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129883398..129885861-chr4:129887383..129889705,3	K562	blood:
2	chr4:129883398..129885861-chr4:129887383..129889506,2	K562	blood:
3	chr4:129886935..129889219-chr4:130012773..130015050,2	K562	blood:

Variant related genes	Relation type
ENSG00000151470	Chromatin interaction
ENSG00000151466	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10028974	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934740	0.83[JPT][hapmap]
rs1376202	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs172168	0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.88[ASN][1000 genomes]
rs1756011	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757926	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1757929	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1757937	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1757938	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757942	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1838911	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs189236	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes]
rs2118045	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2592948	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2597837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2655311	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2777822	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2777823	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs280594	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280596	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs280597	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs280601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3099902	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099903	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3113487	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3113488	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs337276	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs337279	0.90[EUR][1000 genomes]
rs55865936	0.81[ASN][1000 genomes]
rs62316971	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62316978	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6812361	0.83[JPT][hapmap]
rs6824219	0.83[JPT][hapmap]
rs7654405	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs796886	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	79 gene(s)	inside rSNPs	diseases
2	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1026938	chr4:129770961-129936205	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv870175	chr4:129771718-129937945	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1026772	chr4:129773881-129936205	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv461637	chr4:129774375-129924977	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv595397	chr4:129774375-129924977	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv461638	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv595398	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv1018994	chr4:129775612-129933968	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv1034996	chr4:129777825-129905255	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv537249	chr4:129777825-129905255	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv1022446	chr4:129778025-129905116	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv537250	chr4:129778025-129905116	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv1030296	chr4:129778025-129920680	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv537251	chr4:129778025-129920680	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
18	esv2830419	chr4:129785483-129905256	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
19	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers 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
20	nsv1026722	chr4:129801602-129929219	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv537252	chr4:129801602-129929219	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv595399	chr4:129835649-129924852	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv1020327	chr4:129859624-129914665	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11098994	LOC132321	cis	multi-tissue	Pritchard
rs11098994	C4orf33	cis	parietal	SCAN
rs11098994	LOC132321	cis	normal skin	skin_eQTL
rs11098994	SCLT1	cis	cerebellum	SCAN
rs11098994	C4orf33	cis	Artery Tibial	GTEx
rs11098994	C4orf33	cis	lymphoblastoid	seeQTL
rs11098994	C4orf33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129793800-129907200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:129834800-129907400	Weak transcription	Aorta	Aorta
3	chr4:129839800-129907800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:129841000-129907400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:129845400-129907400	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:129845800-129907200	Weak transcription	Ovary	ovary
7	chr4:129847800-129895400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:129855200-129907800	Weak transcription	K562	blood
9	chr4:129855400-129895200	Weak transcription	Fetal Kidney	kidney
10	chr4:129856400-129907200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:129858600-129891200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:129861000-129907200	Weak transcription	Thymus	Thymus
13	chr4:129862400-129924200	Weak transcription	Colonic Mucosa	Colon
14	chr4:129863600-129892000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:129864000-129895400	Weak transcription	NHLF	lung
16	chr4:129864000-129918000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:129864200-129895400	Weak transcription	Fetal Lung	lung
18	chr4:129864400-129901000	Weak transcription	A549	lung
19	chr4:129865600-129907200	Weak transcription	Pancreas	Pancrea
20	chr4:129866400-129888800	Weak transcription	Brain Germinal Matrix	brain
21	chr4:129866400-129907600	Weak transcription	Small Intestine	intestine
22	chr4:129866600-129916600	Weak transcription	Right Ventricle	heart
23	chr4:129866800-129916200	Weak transcription	Hela-S3	cervix
24	chr4:129867000-129907400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:129868200-129935600	Weak transcription	HSMM	muscle
26	chr4:129868400-129890000	Weak transcription	Fetal Stomach	stomach
27	chr4:129868600-129889000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:129868600-129895000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr4:129868600-129907200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:129868600-129907200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:129868600-129907200	Weak transcription	Adipose Nuclei	Adipose
32	chr4:129868600-129907400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr4:129871600-129907600	Weak transcription	Liver	Liver
34	chr4:129873200-129900600	Weak transcription	NHDF-Ad	bronchial
35	chr4:129873800-129900600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:129877400-129907200	Weak transcription	GM12878-XiMat	blood
37	chr4:129877800-129889200	Weak transcription	HUVEC	blood vessel
38	chr4:129878400-129925600	Weak transcription	HSMMtube	muscle
39	chr4:129878600-129907400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:129879400-129895400	Weak transcription	Fetal Intestine Small	intestine
41	chr4:129879800-129906600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr4:129880000-129895200	Weak transcription	Fetal Intestine Large	intestine
43	chr4:129880200-129889800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr4:129883200-129890000	Weak transcription	Dnd41	blood
45	chr4:129883200-129923400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:129883400-129890000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:129883400-129893800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:129883400-129894200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr4:129883400-129907600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:129883400-129912600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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