Variant report

Variant	rs6834455
Chromosome Location	chr4:3113648-3113649
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr4:3113150-3113670	T-47D	breast:	n/a	n/a
2	POLR2A	chr4:3113085-3113709	HUVEC	blood vessel:	n/a	n/a
3	FOS	chr4:3113064-3114515	HUVEC	blood vessel:	n/a	chr4:3113278-3113289
4	EP300	chr4:3113133-3113690	T-47D	breast:	n/a	n/a
5	GATA3	chr4:3113099-3113775	MCF-7	breast:	n/a	n/a
6	POLR2A	chr4:3113517-3113652	MCF-7	breast:	n/a	n/a
7	JUND	chr4:3113107-3113857	T-47D	breast:	n/a	n/a
8	TEAD4	chr4:3113144-3113663	MCF-7	breast:	n/a	n/a
9	POLR2A	chr4:3113433-3113719	MCF-7	breast:	n/a	n/a
10	SRF	chr4:3113159-3113667	MCF-7	breast:	n/a	n/a
11	POLR2A	chr4:3113425-3113919	MCF-7	breast:	n/a	n/a
12	CTCF	chr4:3113560-3113710	HUVEC	blood vessel:	n/a	n/a
13	EP300	chr4:3113125-3113730	MCF-7	breast:	n/a	n/a
14	POLR2A	chr4:3112953-3113711	HUVEC	blood vessel:	n/a	n/a
15	ESR1	chr4:3113107-3113698	T-47D	breast:	n/a	n/a
16	SIN3AK20	chr4:3112892-3113942	MCF-7	breast:	n/a	n/a
17	SIN3AK20	chr4:3113110-3113830	MCF-7	breast:	n/a	n/a
18	ESR1	chr4:3113023-3113678	T-47D	breast:	n/a	n/a
19	GATA3	chr4:3113205-3113703	MCF-7	breast:	n/a	n/a
20	GATA3	chr4:3112938-3113873	MCF-7	breast:	n/a	n/a
21	GATA3	chr4:3113146-3113661	T-47D	breast:	n/a	n/a
22	GATA2	chr4:3113018-3114210	HUVEC	blood vessel:	n/a	n/a
23	ESR1	chr4:3113133-3113665	T-47D	breast:	n/a	n/a
24	ESR1	chr4:3113047-3113729	T-47D	breast:	n/a	n/a
25	TCF12	chr4:3113103-3113698	MCF-7	breast:	n/a	n/a
26	TEAD4	chr4:3113162-3113678	MCF-7	breast:	n/a	n/a
27	HA-E2F1	chr4:3113224-3113859	MCF-7	breast:	n/a	n/a
28	HDAC2	chr4:3113166-3113668	MCF-7	breast:	n/a	n/a
29	EP300	chr4:3113138-3113745	MCF-7	breast:	n/a	n/a
30	TCF12	chr4:3112872-3113886	MCF-7	breast:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:3112586..3114767-chr4:3116395..3118846,2	K562	blood:
2	chr4:3074016..3078502-chr4:3111809..3117809,7	MCF-7	breast:
3	chr4:3108607..3111576-chr4:3111924..3115873,4	MCF-7	breast:
4	chr4:3113077..3115750-chr4:3467353..3469747,2	MCF-7	breast:
5	chr4:3112929..3115298-chr4:3124048..3126368,4	MCF-7	breast:
6	chr4:3112316..3115305-chr4:3484783..3488167,5	MCF-7	breast:
7	chr4:3112475..3121644-chr4:3122211..3126506,10	MCF-7	breast:
8	chr4:3112586..3114555-chr4:3116412..3118846,2	K562	blood:
9	chr4:3101999..3103736-chr4:3111886..3114032,2	MCF-7	breast:
10	chr4:3112733..3115394-chr4:3157286..3160905,3	MCF-7	breast:
11	chr4:3112451..3114098-chr4:3143908..3145762,2	MCF-7	breast:
12	chr14:104159527..104160460-chr4:3112980..3113908,2	MCF-7	breast:
13	chr4:2936679..2938271-chr4:3113488..3115366,2	MCF-7	breast:
14	chr4:3111872..3117206-chr4:3129314..3133133,7	MCF-7	breast:
15	chr4:3075012..3079488-chr4:3111729..3116028,6	MCF-7	breast:
16	chr4:3113073..3113802-chr4:3464660..3465432,3	MCF-7	breast:
17	chr4:3113490..3115240-chr4:3135179..3136981,2	MCF-7	breast:
18	chr4:3108596..3110379-chr4:3112346..3116556,3	K562	blood:
19	chr4:3110927..3117533-chr4:3461507..3465762,15	MCF-7	breast:

No data

Variant related genes	Relation type
HTT	TF binding region
ENSG00000175920	Chromatin interaction
ENSG00000251075	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000197386	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10006373	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012793	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021254	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs10034669	0.88[EUR][1000 genomes]
rs10155264	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10488840	0.88[EUR][1000 genomes]
rs110501	0.83[LWK][hapmap]
rs16844026	1.00[CEU][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs16844028	0.88[EUR][1000 genomes]
rs17780797	0.94[AFR][1000 genomes]
rs2003530	0.86[EUR][1000 genomes]
rs2005787	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071655	0.83[ASW][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs2285086	0.83[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs28436280	0.94[EUR][1000 genomes]
rs28643391	0.90[EUR][1000 genomes]
rs28834148	1.00[ASN][1000 genomes]
rs28867436	0.91[AFR][1000 genomes]
rs3025825	0.87[EUR][1000 genomes]
rs362274	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs362276	0.92[EUR][1000 genomes]
rs362277	0.81[EUR][1000 genomes]
rs362278	0.88[EUR][1000 genomes]
rs362303	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs362304	0.81[EUR][1000 genomes]
rs362310	1.00[CEU][hapmap]
rs362323	0.87[EUR][1000 genomes]
rs362325	0.84[CEU][hapmap]
rs362331	0.98[LWK][hapmap];0.85[YRI][hapmap]
rs362338	1.00[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs363063	0.85[AFR][1000 genomes]
rs363067	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363068	1.00[ASN][1000 genomes]
rs363070	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363082	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs363090	0.95[EUR][1000 genomes]
rs363091	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[EUR][1000 genomes]
rs363093	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363094	0.86[EUR][1000 genomes]
rs363095	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs363097	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363098	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363100	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363101	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs363106	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs363124	0.95[EUR][1000 genomes]
rs363125	0.95[EUR][1000 genomes]
rs363128	0.88[EUR][1000 genomes]
rs363141	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4690072	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs4690073	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs59147561	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61792464	1.00[ASN][1000 genomes]
rs61792535	0.94[EUR][1000 genomes]
rs6446723	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs6446724	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446725	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828882	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829069	1.00[CHD][hapmap]
rs6835567	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839081	0.95[EUR][1000 genomes]
rs6839274	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844859	0.85[YRI][hapmap]
rs7438553	0.85[EUR][1000 genomes]
rs7654034	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7663133	1.00[ASN][1000 genomes]
rs7665816	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667354	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682324	1.00[ASN][1000 genomes]
rs7683309	0.88[EUR][1000 genomes]
rs7688390	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691627	0.83[ASW][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs82333	0.83[LWK][hapmap]
rs916171	0.98[LWK][hapmap];0.89[YRI][hapmap]
rs9993542	1.00[CHD][hapmap]
rs9993781	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6834455	OTOP1	cis	cerebellum	SCAN
rs6834455	SH3BP2	cis	cerebellum	SCAN
rs6834455	TMEM129	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3078600-3113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:3080000-3117800	Weak transcription	Small Intestine	intestine
3	chr4:3088200-3164200	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr4:3094400-3123400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:3097200-3143400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:3097200-3162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:3097400-3163800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:3098000-3162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:3099800-3114400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:3100000-3159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:3101000-3113800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:3101000-3120600	Strong transcription	Fetal Stomach	stomach
13	chr4:3101000-3122600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr4:3101000-3124200	Strong transcription	Fetal Intestine Large	intestine
15	chr4:3101000-3124400	Strong transcription	Thymus	Thymus
16	chr4:3101600-3124200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:3101800-3114400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:3104800-3115200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:3105400-3123800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr4:3105400-3124800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:3105800-3115400	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr4:3105800-3121400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:3106400-3115400	Strong transcription	Fetal Lung	lung
24	chr4:3106400-3123400	Strong transcription	Primary T cells from cord blood	blood
25	chr4:3106400-3123800	Strong transcription	Fetal Thymus	thymus
26	chr4:3106400-3145000	Strong transcription	Dnd41	blood
27	chr4:3106600-3115600	Strong transcription	Fetal Brain Female	brain
28	chr4:3106800-3125200	Strong transcription	Primary B cells from cord blood	blood
29	chr4:3107000-3114200	Strong transcription	HepG2	liver
30	chr4:3108400-3119600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:3108400-3123000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:3108600-3115200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:3108600-3125800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr4:3108600-3136600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:3108600-3163000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr4:3108800-3114000	Strong transcription	Brain Cingulate Gyrus	brain
37	chr4:3108800-3115200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:3108800-3115800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:3108800-3120600	Strong transcription	Fetal Intestine Small	intestine
40	chr4:3108800-3123600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:3108800-3164600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr4:3109000-3114800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr4:3109000-3115000	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr4:3109000-3123200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:3109000-3123600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:3109000-3124200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:3109200-3119600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr4:3109200-3123200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr4:3109200-3142600	Strong transcription	GM12878-XiMat	blood
50	chr4:3109400-3114800	Strong transcription	Placenta	Placenta

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