Variant report

Variant	rs11934397
Chromosome Location	chr4:120376756-120376757
allele	G/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	FOXA1	chr4:120376613-120377159	HepG2	liver:	n/a	n/a
2	TCF12	chr4:120376536-120376916	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:120376632-120377035	GM12878	blood:	n/a	n/a
4	POU2F2	chr4:120374796-120376926	GM12891	blood:	n/a	chr4:120375493-120375505
5	SP1	chr4:120376656-120377230	HepG2	liver:	n/a	n/a
6	POU2F2	chr4:120374395-120377066	GM12878	blood:	n/a	chr4:120375493-120375505
7	POLR2A	chr4:120376729-120377087	Hela-S3	cervix:	n/a	n/a
8	HEY1	chr4:120376605-120377209	HepG2	liver:	n/a	n/a
9	POLR2A	chr4:120376746-120377296	PANC-1	pancreas:	n/a	n/a
10	JUND	chr4:120376727-120376903	HepG2	liver:	n/a	n/a
11	POLR2A	chr4:120376732-120377179	HepG2	liver:	n/a	n/a
12	POLR2A	chr4:120374268-120377037	GM12892	blood:	n/a	n/a
13	FOXA2	chr4:120376639-120377014	A549	lung:	n/a	n/a
14	HEY1	chr4:120375158-120377305	HepG2	liver:	n/a	n/a
15	PAX5	chr4:120376570-120377022	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:120374208-120377141	GM12892	blood:	n/a	n/a
17	FOSL2	chr4:120376724-120376972	HepG2	liver:	n/a	n/a
18	POLR2A	chr4:120376724-120377078	Hela-S3	cervix:	n/a	n/a
19	SIN3AK20	chr4:120376746-120377192	HepG2	liver:	n/a	n/a
20	POLR2A	chr4:120374809-120377349	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr4:120374200-120377199	H1-hESC	embryonic stem cell:	n/a	n/a
22	HEY1	chr4:120376658-120377016	K562	blood:	n/a	n/a
23	PAX5	chr4:120374710-120377019	GM12878	blood:	n/a	n/a
24	IRF4	chr4:120376612-120376936	GM12878	blood:	n/a	n/a
25	POLR2A	chr4:120374265-120377149	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119679216..119681142-chr4:120375525..120377542,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250950	TF binding region
ENSG00000245958	TF binding region
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10004144	0.87[AMR][1000 genomes]
rs10006525	0.86[AMR][1000 genomes]
rs10006706	0.87[AMR][1000 genomes]
rs10006793	0.88[AMR][1000 genomes]
rs10008459	0.87[AMR][1000 genomes]
rs10009450	0.89[AMR][1000 genomes]
rs10017335	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10017389	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10018726	0.87[AMR][1000 genomes]
rs10019406	0.81[AMR][1000 genomes]
rs10019522	0.81[AMR][1000 genomes]
rs10020027	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10026493	0.87[AMR][1000 genomes]
rs10026516	0.89[AMR][1000 genomes]
rs10026736	0.90[AMR][1000 genomes]
rs10026748	0.85[AMR][1000 genomes]
rs10026952	0.89[AMR][1000 genomes]
rs10031483	0.87[AMR][1000 genomes]
rs10031665	0.87[AMR][1000 genomes]
rs10032151	0.89[AMR][1000 genomes]
rs10032158	0.89[AMR][1000 genomes]
rs10034623	0.85[AMR][1000 genomes]
rs10518328	0.87[AMR][1000 genomes]
rs11098524	0.89[AMR][1000 genomes]
rs11098525	0.89[AMR][1000 genomes]
rs11098526	0.90[AMR][1000 genomes]
rs11098527	0.87[AMR][1000 genomes]
rs11098530	0.87[AMR][1000 genomes]
rs11729521	0.87[AMR][1000 genomes]
rs11734241	0.87[AMR][1000 genomes]
rs11934314	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11934328	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11934940	0.90[AMR][1000 genomes]
rs11935596	0.87[AMR][1000 genomes]
rs11940028	0.87[AMR][1000 genomes]
rs11943877	0.89[AMR][1000 genomes]
rs12499324	0.90[AMR][1000 genomes]
rs12502423	0.88[AMR][1000 genomes]
rs12502909	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12505878	0.82[AMR][1000 genomes]
rs12505953	0.90[AMR][1000 genomes]
rs12507964	0.87[AMR][1000 genomes]
rs12508504	0.86[AMR][1000 genomes]
rs12510138	0.88[AMR][1000 genomes]
rs13107475	0.87[AMR][1000 genomes]
rs13145352	0.86[AMR][1000 genomes]
rs1480931	0.87[AMR][1000 genomes]
rs17005535	0.86[AMR][1000 genomes]
rs17006190	0.82[AMR][1000 genomes]
rs17046116	0.89[AMR][1000 genomes]
rs17046118	0.89[AMR][1000 genomes]
rs1809406	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2127821	0.81[AMR][1000 genomes]
rs2306455	0.87[AMR][1000 genomes]
rs2389803	0.87[AMR][1000 genomes]
rs2389809	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28374462	0.89[AMR][1000 genomes]
rs28394590	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28408407	0.85[AMR][1000 genomes]
rs28441656	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28444327	0.89[AMR][1000 genomes]
rs28461559	0.89[AMR][1000 genomes]
rs28479042	0.90[AMR][1000 genomes]
rs28499576	0.87[AMR][1000 genomes]
rs28529639	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28559989	0.89[AMR][1000 genomes]
rs28567426	0.87[AMR][1000 genomes]
rs28571712	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28587142	0.89[AMR][1000 genomes]
rs28587175	0.86[AMR][1000 genomes]
rs28626372	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs28632018	0.89[AMR][1000 genomes]
rs28655325	0.81[AFR][1000 genomes]
rs28665282	0.87[AMR][1000 genomes]
rs28685688	0.84[AMR][1000 genomes]
rs28753180	0.82[AMR][1000 genomes]
rs28845498	0.87[AMR][1000 genomes]
rs2892848	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34004415	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34858317	0.86[AMR][1000 genomes]
rs35063680	0.86[AMR][1000 genomes]
rs3733519	0.87[AMR][1000 genomes]
rs3733520	0.85[AMR][1000 genomes]
rs3733523	0.87[AMR][1000 genomes]
rs3733524	0.84[AMR][1000 genomes]
rs4001185	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4001190	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4001191	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4577559	0.87[AMR][1000 genomes]
rs56270433	0.87[AMR][1000 genomes]
rs66506550	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6822679	0.87[AMR][1000 genomes]
rs6834796	0.87[AMR][1000 genomes]
rs6837828	0.89[AMR][1000 genomes]
rs6838814	0.89[AMR][1000 genomes]
rs6842762	0.87[AMR][1000 genomes]
rs6848389	0.87[AMR][1000 genomes]
rs6849171	0.85[AMR][1000 genomes]
rs6849561	0.87[AMR][1000 genomes]
rs71614438	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs71614443	0.90[AMR][1000 genomes]
rs71614444	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71614448	0.86[AMR][1000 genomes]
rs71614449	0.86[AMR][1000 genomes]
rs71629403	0.86[AMR][1000 genomes]
rs71629404	0.84[AMR][1000 genomes]
rs7436506	0.89[AMR][1000 genomes]
rs7654529	0.89[AMR][1000 genomes]
rs7654546	0.89[AMR][1000 genomes]
rs7654587	0.89[AMR][1000 genomes]
rs7656252	0.87[AMR][1000 genomes]
rs7659336	0.89[AMR][1000 genomes]
rs7659501	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7659551	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7664458	0.86[AMR][1000 genomes]
rs7680704	0.87[AMR][1000 genomes]
rs7681214	0.89[AMR][1000 genomes]
rs7681544	0.87[AMR][1000 genomes]
rs7681978	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7687843	0.87[AMR][1000 genomes]
rs7688613	0.89[AMR][1000 genomes]
rs9993199	0.89[AMR][1000 genomes]
rs9994730	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9994810	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9998585	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv879844	chr4:120341296-120449810	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv879846	chr4:120341296-120491714	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv879847	chr4:120371729-120450159	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11934397	RP11-33B1.1	cis	Whole Blood	GTEx
rs11934397	RP11-33B1.4	cis	Whole Blood	GTEx
rs11934397	RP11-33B1.1	cis	Heart Left Ventricle	GTEx
rs11934397	RP11-33B1.1	cis	lung	GTEx
rs11934397	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs11934397	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs11934397	RP11-384K6.6	cis	Whole Blood	GTEx
rs11934397	RP11-33B1.1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120374800-120377000	Active TSS	Dnd41	blood
2	chr4:120374800-120377400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:120374800-120377400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:120375000-120377000	Active TSS	Placenta	Placenta
5	chr4:120375000-120377200	Active TSS	A549	lung
6	chr4:120375000-120377400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:120375000-120377400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:120375000-120377400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:120375000-120377400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:120375200-120376800	Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr4:120375200-120376800	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr4:120375200-120376800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:120375200-120376800	Active TSS	Fetal Muscle Leg	muscle
14	chr4:120375200-120377000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:120375200-120377000	Active TSS	Primary T cells from cord blood	blood
16	chr4:120375200-120377000	Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr4:120375200-120377000	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr4:120375200-120377000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:120375200-120377000	Active TSS	Liver	Liver
20	chr4:120375200-120377000	Active TSS	Brain Hippocampus Middle	brain
21	chr4:120375200-120377000	Active TSS	Colon Smooth Muscle	Colon
22	chr4:120375200-120377000	Active TSS	Duodenum Mucosa	Duodenum
23	chr4:120375200-120377000	Active TSS	Fetal Muscle Trunk	muscle
24	chr4:120375200-120377000	Active TSS	Pancreas	Pancrea
25	chr4:120375200-120377000	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr4:120375200-120377000	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr4:120375200-120377000	Active TSS	Monocytes-CD14+_RO01746	blood
28	chr4:120375200-120377200	Active TSS	H9 Cell Line	embryonic stem cell
29	chr4:120375200-120377200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:120375200-120377200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:120375200-120377200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:120375200-120377200	Active TSS	Brain Angular Gyrus	brain
33	chr4:120375200-120377200	Active TSS	Brain Anterior Caudate	brain
34	chr4:120375200-120377200	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr4:120375200-120377200	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr4:120375200-120377200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr4:120375200-120377200	Active TSS	Fetal Intestine Small	intestine
38	chr4:120375200-120377200	Active TSS	Right Atrium	heart
39	chr4:120375200-120377200	Active TSS	Right Ventricle	heart
40	chr4:120375200-120377200	Active TSS	NH-A	brain
41	chr4:120375200-120377400	Active TSS	H1 Cell Line	embryonic stem cell
42	chr4:120375200-120377400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:120375200-120377400	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr4:120375200-120377400	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr4:120375200-120377400	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr4:120375200-120377400	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr4:120375200-120377400	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr4:120375200-120377400	Active TSS	Brain Germinal Matrix	brain
49	chr4:120375200-120377400	Active TSS	Colonic Mucosa	Colon
50	chr4:120375200-120377400	Active TSS	Fetal Brain Female	brain

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