Variant report

Variant	rs1894414
Chromosome Location	chr22:29702654-29702655
allele	A/C
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	ELF1	chr22:29702497-29703476	K562	blood:	n/a	n/a
2	GATA3	chr22:29701935-29703097	MCF-7	breast:	n/a	n/a
3	POLR2A	chr22:29702182-29703242	PFSK-1	brain:	n/a	n/a
4	E2F6	chr22:29702075-29702924	K562	blood:	n/a	chr22:29702318-29702325 chr22:29702316-29702327 chr22:29702318-29702325 chr22:29702318-29702325 chr22:29702885-29702894
5	MAX	chr22:29702127-29703191	SK-N-SH	brain:	n/a	chr22:29702885-29702895
6	POLR2A	chr22:29702050-29702931	PBDE	blood:	n/a	n/a
7	MAZ	chr22:29702058-29703657	Hela-S3	cervix:	n/a	chr22:29702885-29702895
8	TAF1	chr22:29702410-29702783	K562	blood:	n/a	n/a
9	BCL3	chr22:29702547-29703058	A549	lung:	n/a	chr22:29702569-29702582 chr22:29702914-29702927
10	MAX	chr22:29701922-29703739	A549	lung:	n/a	chr22:29702885-29702895
11	EP300	chr22:29702124-29703272	K562	blood:	n/a	chr22:29702293-29702309 chr22:29702299-29702315 chr22:29702257-29702273 chr22:29702914-29702930 chr22:29702283-29702299
12	TCF12	chr22:29701819-29703578	ECC-1	luminal epithelium:	n/a	chr22:29702870-29702878 chr22:29702992-29703000 chr22:29702074-29702084
13	MAZ	chr22:29702080-29703349	K562	blood:	n/a	chr22:29702885-29702895
14	SIN3A	chr22:29702095-29703026	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr22:29702090-29703706	SK-N-MC	brain:	n/a	n/a
16	HCFC1	chr22:29701861-29703393	Hela-S3	cervix:	n/a	n/a
17	NR3C1	chr22:29702423-29702896	A549	lung:	n/a	chr22:29702664-29702680 chr22:29702661-29702682 chr22:29702664-29702680 chr22:29702665-29702679
18	POLR2A	chr22:29701983-29703175	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr22:29702620-29702655	MCF-7	breast:	n/a	n/a
20	JUND	chr22:29702206-29702758	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr22:29702046-29703418	Hela-S3	cervix:	n/a	chr22:29702885-29702895
22	CTBP2	chr22:29702009-29703073	H1-hESC	embryonic stem cell:	n/a	n/a
23	NR3C1	chr22:29702487-29702787	ECC-1	luminal epithelium:	n/a	chr22:29702664-29702680 chr22:29702661-29702682 chr22:29702664-29702680 chr22:29702665-29702679
24	CTCF	chr22:29701947-29703979	SK-N-SH	brain:	n/a	chr22:29702302-29702315
25	TAF1	chr22:29702189-29702829	K562	blood:	n/a	n/a
26	ELK1	chr22:29702467-29702860	K562	blood:	n/a	n/a
27	MAX	chr22:29702075-29703196	SK-N-SH	brain:	n/a	chr22:29702885-29702895
28	CEBPB	chr22:29702568-29702659	H1-hESC	embryonic stem cell:	n/a	n/a
29	NR3C1	chr22:29702531-29703230	ECC-1	luminal epithelium:	n/a	chr22:29702664-29702680 chr22:29702661-29702682 chr22:29702664-29702680 chr22:29702665-29702679
30	HA-E2F1	chr22:29702076-29703218	Hela-S3	cervix:	n/a	chr22:29702318-29702325 chr22:29702256-29702267 chr22:29702999-29703008 chr22:29702318-29702325 chr22:29702318-29702325 chr22:29702885-29702894
31	HDAC2	chr22:29702071-29702657	MCF-7	breast:	n/a	n/a
32	POLR2A	chr22:29702521-29702945	H1-hESC	embryonic stem cell:	n/a	n/a
33	REST	chr22:29702170-29702743	K562	blood:	n/a	chr22:29702287-29702305
34	MAX	chr22:29702063-29703162	MCF-7	breast:	n/a	chr22:29702885-29702895
35	HEY1	chr22:29702264-29702874	K562	blood:	n/a	n/a
36	MAX	chr22:29701917-29703687	HepG2	liver:	n/a	chr22:29702885-29702895
37	REST	chr22:29702562-29702704	K562	blood:	n/a	n/a
38	KAP1	chr22:29701971-29702746	HEK293	kidney:	n/a	n/a
39	MAX	chr22:29701829-29703686	ECC-1	luminal epithelium:	n/a	chr22:29702885-29702895
40	NR3C1	chr22:29702516-29702805	A549	lung:	n/a	chr22:29702664-29702680 chr22:29702661-29702682 chr22:29702664-29702680 chr22:29702665-29702679
41	CREB1	chr22:29702537-29703206	A549	lung:	n/a	n/a
42	YY1	chr22:29702024-29702720	SK-N-SH	brain:	n/a	chr22:29702231-29702242
43	CTCF	chr22:29702640-29702790	GM12875	blood:	n/a	n/a
44	TBP	chr22:29702076-29703096	K562	blood:	n/a	n/a
45	CHD2	chr22:29702654-29702754	K562	blood:	n/a	n/a
46	POLR2A	chr22:29702323-29703095	K562	blood:	n/a	n/a
47	TFAP2C	chr22:29701978-29703656	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr22:29702534-29702748	SK-N-SH	brain:	n/a	n/a
49	FOXM1	chr22:29702040-29702756	MCF-7	breast:	n/a	n/a
50	ZNF263	chr22:29702015-29702965	HEK293-T-REx	kidney:	n/a	chr22:29702736-29702745 chr22:29702610-29702619

No.	Distal block	Cell Line	Cell type
1	chr22:29702549..29705407-chr22:29734900..29738437,3	MCF-7	breast:
2	chr22:29661955..29666922-chr22:29700529..29704114,10	K562	blood:
3	chr22:29660929..29666447-chr22:29700529..29705135,9	K562	blood:
4	chr22:29700857..29704420-chr22:29708764..29712339,6	MCF-7	breast:
5	chr22:29685583..29688004-chr22:29700889..29703726,2	MCF-7	breast:
6	chr22:29670501..29673200-chr22:29700972..29703163,2	K562	blood:
7	chr22:29701804..29704290-chr22:29781998..29785634,5	MCF-7	breast:
8	chr22:29663358..29665751-chr22:29702504..29704805,4	MCF-7	breast:
9	chr22:29702481..29704174-chr22:29874105..29876353,2	K562	blood:

Variant related genes	Relation type
GAS2L1	TF binding region
ENSG00000100276	Chromatin interaction
ENSG00000225465	Chromatin interaction
ENSG00000100263	Chromatin interaction
ENSG00000182944	Chromatin interaction
ENSG00000100285	Chromatin interaction
ENSG00000100280	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11702906	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11703897	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11704551	0.81[ASW][hapmap];0.86[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs11705446	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs131184	0.89[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs131190	0.89[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs140064	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs140065	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.91[EUR][1000 genomes]
rs174760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs174768	1.00[JPT][hapmap]
rs174772	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2231398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2518683	0.82[CHB][hapmap];0.87[CHD][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap]
rs2857460	0.90[EUR][1000 genomes]
rs2857464	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34680030	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4823033	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5997460	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7285200	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8140836	0.81[ASW][hapmap];0.86[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv829155	chr22:29664396-29724001	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv914959	chr22:29696438-29712874	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv914960	chr22:29696438-29714069	Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1894414	NEFH	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29702000-29702800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
2	chr22:29702000-29702800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr22:29702000-29702800	Flanking Active TSS	Liver	Liver
4	chr22:29702000-29702800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
5	chr22:29702000-29702800	Flanking Active TSS	Pancreas	Pancrea
6	chr22:29702000-29702800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr22:29702000-29702800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr22:29702000-29702800	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr22:29702000-29702800	Flanking Bivalent TSS/Enh	Dnd41	blood
10	chr22:29702000-29703000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
11	chr22:29702000-29703000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr22:29702000-29703200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
13	chr22:29702000-29703400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr22:29702000-29703600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr22:29702000-29703600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr22:29702000-29703600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr22:29702000-29703600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
18	chr22:29702000-29703800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr22:29702000-29704000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr22:29702000-29704000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr22:29702000-29704400	Flanking Active TSS	Colonic Mucosa	Colon
22	chr22:29702000-29705600	Active TSS	Fetal Brain Female	brain
23	chr22:29702000-29707800	Enhancers	Fetal Heart	heart
24	chr22:29702200-29702800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr22:29702200-29702800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
26	chr22:29702200-29702800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr22:29702200-29702800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
28	chr22:29702200-29702800	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
29	chr22:29702200-29702800	Flanking Active TSS	Fetal Intestine Small	intestine
30	chr22:29702200-29702800	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr22:29702200-29702800	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr22:29702200-29702800	Flanking Active TSS	Placenta	Placenta
33	chr22:29702200-29703000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
34	chr22:29702200-29703000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr22:29702200-29703000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
36	chr22:29702200-29703200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr22:29702200-29703200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr22:29702200-29703200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
39	chr22:29702200-29703200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr22:29702200-29703400	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr22:29702200-29703400	Active TSS	H1 Cell Line	embryonic stem cell
42	chr22:29702200-29703400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr22:29702200-29703400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr22:29702200-29703400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr22:29702200-29703400	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr22:29702200-29703400	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr22:29702200-29703400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr22:29702200-29703400	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr22:29702200-29703400	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr22:29702200-29703400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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