Variant report

Variant	rs35902101
Chromosome Location	chr11:47795169-47795170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47788346..47792953-chr11:47794926..47797941,5	K562	blood:

Variant related genes	Relation type
ENSG00000109920	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10838747	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838748	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838757	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039342	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039348	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11039355	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039389	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039416	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039426	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039433	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11602339	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11602395	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11604825	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11605774	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12361031	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12364432	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12418852	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12421210	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12785833	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12787112	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12787330	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12787646	0.84[EUR][1000 genomes]
rs12798109	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12803191	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17788930	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2290850	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34128973	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34910028	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34923397	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35805829	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35985502	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752797	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752873	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7105282	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7120333	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7130758	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7927771	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7947730	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9909	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs35902101	C1QTNF4	cis	Muscle Skeletal	GTEx
rs35902101	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs35902101	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs35902101	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs35902101	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs35902101	C1QTNF4	cis	lung	GTEx
rs35902101	C1QTNF4	cis	Whole Blood	GTEx
rs35902101	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47789600-47796600	Weak transcription	Lung	lung
2	chr11:47789800-47798600	Weak transcription	Ovary	ovary
3	chr11:47790000-47797200	Weak transcription	Gastric	stomach
4	chr11:47790000-47798800	Weak transcription	Colonic Mucosa	Colon
5	chr11:47790000-47800200	Weak transcription	Psoas Muscle	Psoas
6	chr11:47790000-47800200	Weak transcription	Stomach Mucosa	stomach
7	chr11:47790000-47806800	Weak transcription	Esophagus	oesophagus
8	chr11:47790000-47837800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:47790200-47795200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:47790200-47796000	Weak transcription	Fetal Lung	lung
11	chr11:47790200-47796200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:47790200-47796200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:47790200-47796200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr11:47790200-47796200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:47790200-47796200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:47790200-47796200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:47790200-47796400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:47790200-47796400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:47790200-47796400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:47790200-47796600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:47790200-47796600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:47790200-47796600	Weak transcription	Aorta	Aorta
23	chr11:47790200-47796800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:47790200-47796800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr11:47790200-47796800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:47790200-47798400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:47790200-47798600	Weak transcription	Pancreas	Pancrea
28	chr11:47790200-47798800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:47790200-47798800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:47790200-47798800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:47790200-47798800	Weak transcription	Right Ventricle	heart
32	chr11:47790200-47799000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:47790200-47801000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:47790200-47801600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr11:47790200-47805200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr11:47790200-47869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr11:47790400-47795400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:47790400-47795600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:47790400-47796000	Weak transcription	Thymus	Thymus
40	chr11:47790400-47796200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:47790400-47796200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr11:47790400-47796200	Weak transcription	Primary T cells from cord blood	blood
43	chr11:47790400-47796200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:47790400-47796200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:47790400-47796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:47790400-47796200	Weak transcription	Fetal Brain Female	brain
47	chr11:47790400-47796200	Weak transcription	Placenta	Placenta
48	chr11:47790400-47796200	Weak transcription	Fetal Stomach	stomach
49	chr11:47790400-47796200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr11:47790400-47796200	Weak transcription	Rectal Mucosa Donor 29	rectum

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