Variant report

Variant	rs4930737
Chromosome Location	chr12:124139597-124139598
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	RUNX3	chr12:124139587-124140368	GM12878	blood:	n/a	n/a
2	EBF1	chr12:124139597-124139769	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:124137919..124140915-chr12:124140949..124142983,2	MCF-7	breast:
2	chr12:124138422..124140008-chr12:124142075..124144430,2	MCF-7	breast:
3	chr12:124137852..124140530-chr12:124458317..124460698,2	K562	blood:

Variant related genes	Relation type
GTF2H3	TF binding region
ENSG00000111358	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1050443	0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs1050448	1.00[JPT][hapmap]
rs1060637	0.85[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1060639	0.81[AFR][1000 genomes]
rs10744158	0.84[CEU][hapmap]
rs10744162	1.00[JPT][hapmap]
rs10773034	1.00[JPT][hapmap]
rs11572910	0.82[LWK][hapmap]
rs11572920	0.81[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11572952	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11612927	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs11615162	0.82[AFR][1000 genomes]
rs12809853	1.00[JPT][hapmap]
rs12816883	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12817576	0.86[AFR][1000 genomes]
rs12830927	0.86[YRI][hapmap]
rs1515815	0.85[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs15587	1.00[JPT][hapmap]
rs1962020	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3204541	1.00[JPT][hapmap]
rs35804181	0.82[AFR][1000 genomes]
rs36018806	0.86[AFR][1000 genomes]
rs6488878	1.00[JPT][hapmap]
rs7974279	1.00[JPT][hapmap]
rs7980060	0.83[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	34 gene(s)	inside rSNPs	diseases
5	nsv1040356	chr12:124094758-124172731	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv2757517	chr12:124110122-124195856	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv2759918	chr12:124110122-124195856	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv1041918	chr12:124115035-124184855	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
9	nsv1042866	chr12:124115035-124195856	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv442292	chr12:124115047-124195854	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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
11	esv35148	chr12:124119120-124196120	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	esv2756516	chr12:124119120-124196120	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv1053101	chr12:124119155-124172731	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
14	nsv524660	chr12:124119983-124194438	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv455733	chr12:124119983-124195856	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv560496	chr12:124119983-124195856	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv1040119	chr12:124122376-124152950	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
18	nsv1036843	chr12:124122376-124169697	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
19	nsv1052065	chr12:124127003-124157939	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
20	nsv1051385	chr12:124127003-124160021	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
21	nsv1053923	chr12:124127003-124162750	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
22	nsv1037556	chr12:124127003-124166978	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
23	nsv1043738	chr12:124127003-124169697	Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
24	nsv1046151	chr12:124127003-124172731	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
25	nsv1045476	chr12:124127003-124174020	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
26	nsv1055052	chr12:124127003-124176120	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
27	nsv1044734	chr12:124127003-124179417	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
28	nsv560497	chr12:124129460-124195856	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	nsv560498	chr12:124129924-124195856	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4930737	TCTN2	cis	Nerve Tibial	GTEx
rs4930737	TCTN2	cis	Adipose Subcutaneous	GTEx
rs4930737	ATP6V0A2	cis	parietal	SCAN
rs4930737	TCTN2	cis	parietal	SCAN
rs4930737	DDX55	cis	Liver	GTEx
rs4930737	TCTN2	cis	Artery Tibial	GTEx
rs4930737	TCTN2	cis	lung	GTEx
rs4930737	RNF10	cis	cerebellum	SCAN
rs4930737	EIF2B1	cis	multi-tissue	Pritchard
rs4930737	TCTN2	cis	cerebellum	SCAN
rs4930737	TCTN2	cis	Muscle Skeletal	GTEx
rs4930737	TCTN2	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124119200-124141000	Weak transcription	Aorta	Aorta
2	chr12:124119200-124155200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:124119600-124140600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:124119600-124143000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:124119800-124146200	Weak transcription	Psoas Muscle	Psoas
6	chr12:124119800-124155200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:124121400-124144000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:124123200-124142600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:124123800-124142600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:124124000-124145600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:124124000-124146400	Strong transcription	Fetal Thymus	thymus
12	chr12:124124000-124148200	Strong transcription	Primary T cells from cord blood	blood
13	chr12:124125000-124146600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:124125600-124146800	Weak transcription	Small Intestine	intestine
15	chr12:124126200-124142600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:124126200-124148200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:124126400-124142400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:124126800-124142600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:124126800-124145800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:124126800-124148000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:124127000-124145800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:124127400-124142600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:124129200-124147800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:124129600-124142400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:124129600-124142400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:124129600-124142600	Strong transcription	Liver	Liver
27	chr12:124129600-124143000	Strong transcription	Brain Hippocampus Middle	brain
28	chr12:124129600-124145200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:124129600-124146400	Strong transcription	Dnd41	blood
30	chr12:124129800-124141800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr12:124130000-124141600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:124130800-124141000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:124131000-124155400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:124131200-124151600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:124131200-124155200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:124131400-124141000	Weak transcription	Pancreas	Pancrea
37	chr12:124131400-124155200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr12:124131400-124155200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:124131400-124155600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:124131400-124155600	Weak transcription	Right Ventricle	heart
41	chr12:124132200-124144000	Strong transcription	Osteobl	bone
42	chr12:124132200-124145800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:124133000-124155200	Weak transcription	Stomach Mucosa	stomach
44	chr12:124133600-124145200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:124133800-124142000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:124134000-124141000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr12:124134800-124142400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:124135000-124140600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr12:124135000-124140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:124135000-124141000	Weak transcription	Gastric	stomach

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