Variant report

Variant	rs4147202
Chromosome Location	chr1:197885543-197885544
allele	A/G
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	SUZ12	chr1:197877431-197889818	NT2-D1	testis:	n/a	n/a
2	ZNF263	chr1:197884061-197887474	HEK293-T-REx	kidney:	n/a	chr1:197887374-197887383 chr1:197884671-197884680 chr1:197885944-197885953
3	SIN3A	chr1:197885017-197885570	H1-hESC	embryonic stem cell:	n/a	chr1:197885096-197885107
4	CHD2	chr1:197885050-197885551	Hela-S3	cervix:	n/a	n/a
5	KAP1	chr1:197884827-197885810	U2OS	brain:	n/a	n/a
6	POLR2A	chr1:197885136-197885612	MCF-7	breast:	n/a	n/a
7	HA-E2F1	chr1:197884318-197886407	MCF-7	breast:	n/a	chr1:197885162-197885174 chr1:197885577-197885587
8	KAP1	chr1:197884676-197886575	HEK293	kidney:	n/a	chr1:197885951-197885959
9	MAX	chr1:197884882-197885744	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr1:197885400-197885550	AG04449	skin:	n/a	n/a
11	MAX	chr1:197884545-197885769	NB4	blood:	n/a	chr1:197884571-197884581 chr1:197884572-197884579
12	MYC	chr1:197885512-197885561	MCF-7	breast:	n/a	n/a
13	RAD21	chr1:197884855-197885875	IMR90	lung:	n/a	n/a
14	SUZ12	chr1:197877495-197890009	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr1:197884907-197885894	ECC-1	luminal epithelium:	n/a	n/a
16	RAD21	chr1:197884720-197885783	SK-N-SH	brain:	n/a	n/a
17	HMGN3	chr1:197885042-197885558	K562	blood:	n/a	n/a
18	E2F6	chr1:197884856-197885673	A549	lung:	n/a	chr1:197885162-197885174 chr1:197885577-197885587
19	MAX	chr1:197884837-197885811	A549	lung:	n/a	n/a
20	CTCF	chr1:197883892-197885882	A549	lung:	n/a	chr1:197884909-197884918 chr1:197884514-197884522 chr1:197884911-197884921
21	RCOR1	chr1:197885515-197885567	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:197884793-197889357	H1-neurons	neurons:	n/a	n/a
23	RAD21	chr1:197884866-197885642	ECC-1	luminal epithelium:	n/a	n/a
24	SIN3AK20	chr1:197884965-197885547	SK-N-SH	brain:	n/a	n/a
25	CTBP2	chr1:197884918-197885722	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr1:197884588-197886986	SK-N-SH	brain:	n/a	chr1:197884909-197884918 chr1:197884911-197884921
27	CTCF	chr1:197885400-197885550	WERI-Rb-1	eye:	n/a	n/a
28	MAX	chr1:197884908-197885809	ECC-1	luminal epithelium:	n/a	n/a
29	SMC3	chr1:197884216-197885680	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:197884876..197885553-chr16:2826918..2827685,2	Hela-S3	cervix:
2	chr1:197870101..197873220-chr1:197881150..197886265,4	MCF-7	breast:
3	chr1:197868383..197873929-chr1:197879774..197886951,11	K562	blood:

Variant related genes	Relation type
LHX9	TF binding region
ENSG00000103363	Chromatin interaction
ENSG00000203724	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10922333	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10922334	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11577674	0.93[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12024850	0.92[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12046958	0.93[CEU][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12727777	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12729300	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12750987	0.93[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1909507	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2358777	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34100116	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3894699	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999662	chr1:197821769-197892803	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	esv2762214	chr1:197821769-197897496	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4147202	KCNT2	cis	cerebellum	SCAN
rs4147202	DENND1B	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197884400-197885600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:197884400-197885800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
3	chr1:197884400-197887000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
4	chr1:197884400-197887400	Active TSS	Hela-S3	cervix
5	chr1:197884600-197885600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
6	chr1:197884600-197885600	Bivalent/Poised TSS	A549	lung
7	chr1:197884600-197885800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:197884600-197885800	Bivalent Enhancer	Liver	Liver
9	chr1:197884600-197886600	Bivalent Enhancer	Brain Angular Gyrus	brain
10	chr1:197884600-197887000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
11	chr1:197884600-197887000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr1:197884600-197887000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:197884600-197887400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:197884600-197891000	Bivalent Enhancer	Fetal Thymus	thymus
15	chr1:197884800-197885600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:197884800-197885600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
17	chr1:197884800-197885600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
18	chr1:197884800-197885600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:197884800-197885600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:197884800-197885600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:197884800-197885600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
22	chr1:197884800-197885600	Bivalent Enhancer	Fetal Intestine Large	intestine
23	chr1:197884800-197885800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:197884800-197885800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:197884800-197885800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
26	chr1:197884800-197885800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
27	chr1:197884800-197885800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:197884800-197885800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:197884800-197885800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
30	chr1:197884800-197886000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
31	chr1:197884800-197886000	Enhancers	Spleen	Spleen
32	chr1:197884800-197886200	Bivalent/Poised TSS	HSMMtube	muscle
33	chr1:197884800-197886200	Flanking Bivalent TSS/Enh	NHEK	skin
34	chr1:197884800-197886400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
35	chr1:197884800-197887000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:197884800-197887000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
37	chr1:197884800-197887000	Enhancers	Lung	lung
38	chr1:197884800-197887000	Enhancers	Pancreas	Pancrea
39	chr1:197884800-197887200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
40	chr1:197884800-197887200	Bivalent Enhancer	Fetal Lung	lung
41	chr1:197884800-197887200	Bivalent Enhancer	Stomach Mucosa	stomach
42	chr1:197884800-197887400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:197884800-197887600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:197884800-197887800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
45	chr1:197884800-197887800	Bivalent/Poised TSS	NHDF-Ad	bronchial
46	chr1:197885000-197885600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:197885000-197885600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
48	chr1:197885000-197885600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:197885000-197885600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:197885000-197885600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--

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