Variant report

Variant	rs6848637
Chromosome Location	chr4:165877963-165877964
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	POLR2A	chr4:165877518-165880399	MCF10A-Er-Src	breast:	n/a	n/a
2	TAF1	chr4:165877848-165878321	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:165877824-165878340	H1-hESC	embryonic stem cell:	n/a	n/a
4	RCOR1	chr4:165877925-165878218	K562	blood:	n/a	n/a
5	TBP	chr4:165877783-165878314	GM12878	blood:	n/a	n/a
6	TBP	chr4:165877852-165878554	H1-hESC	embryonic stem cell:	n/a	n/a
7	HCFC1	chr4:165877911-165878279	K562	blood:	n/a	n/a
8	CHD2	chr4:165877922-165878553	H1-hESC	embryonic stem cell:	n/a	n/a
9	GABPA	chr4:165877836-165878297	GM12878	blood:	n/a	n/a
10	REST	chr4:165877810-165878067	PANC-1	pancreas:	n/a	chr4:165877876-165877889
11	WRNIP1	chr4:165877903-165878377	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:165877814-165878285	GM12891	blood:	n/a	n/a
13	MAX	chr4:165877808-165878295	K562	blood:	n/a	n/a
14	RELA	chr4:165877829-165878521	GM15510	blood:	n/a	n/a
15	YY1	chr4:165877805-165878588	H1-hESC	embryonic stem cell:	n/a	n/a
16	TAF1	chr4:165877825-165878500	MCF-7	breast:	n/a	n/a
17	MAX	chr4:165877742-165878603	A549	lung:	n/a	n/a
18	POU2F2	chr4:165877854-165878087	GM12878	blood:	n/a	n/a
19	RELA	chr4:165877841-165878394	GM19099	blood:	n/a	n/a
20	FOXM1	chr4:165877782-165878207	GM12878	blood:	n/a	n/a
21	EBF1	chr4:165877817-165878122	GM12878	blood:	n/a	chr4:165877981-165877992 chr4:165878021-165878032
22	POLR2A	chr4:165877794-165878354	SK-N-SH	brain:	n/a	n/a
23	MYC	chr4:165877787-165878639	MCF10A-Er-Src	breast:	n/a	n/a
24	ELF1	chr4:165877799-165878471	MCF-7	breast:	n/a	chr4:165878105-165878116 chr4:165878104-165878117 chr4:165878106-165878115 chr4:165878105-165878116
25	POLR2A	chr4:165877756-165878741	GM19193	blood:	n/a	n/a
26	ELF1	chr4:165877825-165878341	K562	blood:	n/a	chr4:165878105-165878116 chr4:165878104-165878117 chr4:165878106-165878115 chr4:165878105-165878116
27	PML	chr4:165877796-165878369	MCF-7	breast:	n/a	n/a
28	POLR2A	chr4:165877785-165878416	GM12891	blood:	n/a	n/a
29	RUNX3	chr4:165877798-165878482	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:165877693-165878616	MCF-7	breast:	n/a	n/a
31	CHD2	chr4:165877860-165878562	GM12878	blood:	n/a	n/a
32	ZNF143	chr4:165877917-165878454	H1-hESC	embryonic stem cell:	n/a	n/a
33	GABPA	chr4:165877606-165878746	MCF-7	breast:	n/a	n/a
34	E2F6	chr4:165877701-165878689	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr4:165877850-165878319	A549	lung:	n/a	n/a
36	ZNF143	chr4:165877867-165878563	GM12878	blood:	n/a	n/a
37	POLR2A	chr4:165877773-165878682	GM18526	blood:	n/a	n/a
38	POU2F2	chr4:165877771-165878296	GM12891	blood:	n/a	n/a
39	NFYB	chr4:165877646-165878338	GM12878	blood:	n/a	n/a
40	JUND	chr4:165877934-165878261	K562	blood:	n/a	n/a
41	NFYB	chr4:165877873-165878407	K562	blood:	n/a	n/a
42	PML	chr4:165877652-165878776	GM12878	blood:	n/a	n/a
43	EBF1	chr4:165877819-165878246	GM12878	blood:	n/a	chr4:165877981-165877992 chr4:165878021-165878032
44	GABPA	chr4:165877944-165878428	H1-hESC	embryonic stem cell:	n/a	n/a
45	NFIC	chr4:165877681-165878331	GM12878	blood:	n/a	n/a
46	GABPA	chr4:165877715-165878512	SK-N-SH	brain:	n/a	n/a
47	REST	chr4:165877705-165878681	H1-neurons	neurons:	n/a	chr4:165877876-165877889
48	POLR2A	chr4:165877784-165878500	HL-60	blood:	n/a	n/a
49	MAX	chr4:165877833-165878622	MCF-7	breast:	n/a	n/a
50	POLR2A	chr4:165877753-165878751	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:165868972..165872041-chr4:165876298..165879460,3	MCF-7	breast:
2	chr4:165876074..165878048-chr4:165892405..165894471,2	MCF-7	breast:

Variant related genes	Relation type
FAM218A	TF binding region
ENSG00000236941	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10001548	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10016502	0.89[ASN][1000 genomes]
rs10020142	0.88[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs10020204	0.88[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs10025595	0.85[ASN][1000 genomes]
rs10034083	1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11100586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11936657	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11941364	0.89[ASN][1000 genomes]
rs12501482	0.85[ASN][1000 genomes]
rs12505213	0.88[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs12510353	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12510406	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17584656	0.88[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs2280326	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs28475532	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28544252	0.88[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs28548593	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581275	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28624277	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28631315	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28633542	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3196673	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4286486	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4350966	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4359860	0.88[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs4380479	0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4396952	0.89[ASN][1000 genomes]
rs4511961	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56231925	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6536884	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6536885	0.88[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs6814756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827270	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828659	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847301	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs6856935	0.86[JPT][hapmap]
rs7654142	0.85[CHD][hapmap]
rs7663962	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs7680569	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019150	chr4:165505585-165907924	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv880382	chr4:165793001-165964290	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	esv2757965	chr4:165801816-165976350	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv2759299	chr4:165801816-165976350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv528686	chr4:165814359-165930168	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv967697	chr4:165843736-165889668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1015970	chr4:165852926-165973078	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv830140	chr4:165855999-165956612	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv517554	chr4:165859951-165878335	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
15	esv2760876	chr4:165861386-165893486	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	esv20237	chr4:165861441-165883885	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
17	nsv10607	chr4:165861465-165886549	Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
18	esv3692850	chr4:165868229-165879381	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
19	esv2421831	chr4:165868229-165882293	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6848637	FAM218A	cis	Thyroid	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165874000-165878000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:165877200-165879000	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr4:165877400-165878800	Active TSS	Primary T cells from cord blood	blood
4	chr4:165877400-165879000	Active TSS	Stomach Smooth Muscle	stomach
5	chr4:165877600-165878000	Active TSS	Right Atrium	heart
6	chr4:165877600-165878400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:165877600-165878400	Active TSS	Fetal Stomach	stomach
8	chr4:165877600-165878600	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr4:165877600-165878600	Active TSS	Colon Smooth Muscle	Colon
10	chr4:165877600-165878800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr4:165877600-165878800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:165877600-165878800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:165877600-165878800	Active TSS	Fetal Brain Female	brain
14	chr4:165877600-165878800	Active TSS	Fetal Intestine Small	intestine
15	chr4:165877600-165879000	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr4:165877600-165879000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:165877600-165879000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr4:165877600-165879000	Active TSS	A549	lung
19	chr4:165877600-165879200	Active TSS	NHDF-Ad	bronchial
20	chr4:165877600-165879400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr4:165877600-165879400	Active TSS	Brain Hippocampus Middle	brain
22	chr4:165877600-165879600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:165877600-165879600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:165877600-165879800	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr4:165877600-165880000	Active TSS	Brain Germinal Matrix	brain
26	chr4:165877600-165880200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:165877600-165880200	Active TSS	HSMM	muscle
28	chr4:165877600-165880400	Active TSS	HSMMtube	muscle
29	chr4:165877800-165878000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
30	chr4:165877800-165878000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:165877800-165878000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:165877800-165878000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr4:165877800-165878000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:165877800-165878000	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr4:165877800-165878000	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr4:165877800-165878000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr4:165877800-165878000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:165877800-165878000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr4:165877800-165878000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:165877800-165878000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr4:165877800-165878000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr4:165877800-165878000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr4:165877800-165878000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:165877800-165878000	Active TSS	Esophagus	oesophagus
45	chr4:165877800-165878000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
46	chr4:165877800-165878000	Flanking Active TSS	Placenta	Placenta
47	chr4:165877800-165878000	Flanking Active TSS	Fetal Thymus	thymus
48	chr4:165877800-165878000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr4:165877800-165878000	Flanking Active TSS	Stomach Mucosa	stomach
50	chr4:165877800-165878000	Active TSS	Spleen	Spleen

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