Variant report

Variant	rs37974
Chromosome Location	chr7:8010386-8010387
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	POLR2A	chr7:8007164-8012302	GM12878	blood:	n/a	n/a
2	RAD21	chr7:8010246-8010989	SK-N-SH_RA	brain:	n/a	chr7:8010822-8010831 chr7:8010835-8010849
3	SMC3	chr7:8009352-8011118	Hela-S3	cervix:	n/a	n/a
4	SIN3A	chr7:8007872-8010871	H1-hESC	embryonic stem cell:	n/a	chr7:8008206-8008219 chr7:8008208-8008219
5	MTA3	chr7:8010108-8011175	GM12878	blood:	n/a	n/a
6	RELA	chr7:8009516-8010879	GM19099	blood:	n/a	n/a
7	POLR2A	chr7:8010165-8011527	Hela-S3	cervix:	n/a	n/a
8	MXI1	chr7:8006814-8014285	SK-N-SH	brain:	n/a	n/a
9	MAZ	chr7:8007718-8010413	IMR90	lung:	n/a	chr7:8008789-8008799 chr7:8008803-8008813
10	EP300	chr7:8010333-8010399	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:8006896-8012163	GM12891	blood:	n/a	n/a
12	CHD1	chr7:8007292-8013431	GM12878	blood:	n/a	chr7:8008401-8008411 chr7:8008924-8008934 chr7:8008931-8008941 chr7:8008787-8008797
13	ZNF263	chr7:8007831-8012241	HEK293-T-REx	kidney:	n/a	chr7:8011925-8011934 chr7:8008196-8008205 chr7:8011226-8011235 chr7:8008843-8008852 chr7:8010817-8010826
14	SIN3AK20	chr7:8010133-8010447	PFSK-1	brain:	n/a	n/a
15	SIN3A	chr7:8010129-8010405	GM12878	blood:	n/a	n/a
16	RUNX3	chr7:8010029-8010508	GM12878	blood:	n/a	n/a
17	RCOR1	chr7:8010156-8010968	GM12878	blood:	n/a	n/a
18	POLR2A	chr7:8010033-8010994	GM12891	blood:	n/a	n/a
19	REST	chr7:8007936-8010874	H1-neurons	neurons:	n/a	chr7:8008404-8008414 chr7:8008595-8008608 chr7:8008492-8008505 chr7:8008196-8008209
20	PML	chr7:8007235-8010419	GM12878	blood:	n/a	n/a
21	RAD21	chr7:8010326-8010913	SK-N-SH_RA	brain:	n/a	chr7:8010822-8010831 chr7:8010835-8010849
22	POLR2A	chr7:8006815-8012265	GM12892	blood:	n/a	n/a
23	POLR2A	chr7:8010254-8010560	Hela-S3	cervix:	n/a	n/a
24	NFATC1	chr7:8010296-8012191	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:8007254-8010829	GM12892	blood:	n/a	n/a
26	TAF1	chr7:8010282-8010516	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr7:8009267-8011649	H1-neurons	neurons:	n/a	n/a
28	TBP	chr7:8010251-8011099	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr7:8006934-8012236	GM18505	blood:	n/a	n/a
30	USF2	chr7:8010263-8010550	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr7:8006829-8012192	GM12892	blood:	n/a	n/a
32	POLR2A	chr7:8010268-8011008	H1-neurons	neurons:	n/a	n/a
33	TBL1XR1	chr7:8010198-8011440	GM12878	blood:	n/a	n/a
34	POLR2A	chr7:8010204-8011095	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr7:8007655-8011507	GM18526	blood:	n/a	n/a
36	ATF2	chr7:8009986-8010622	GM12878	blood:	n/a	n/a
37	RCOR1	chr7:8010364-8010945	Hela-S3	cervix:	n/a	n/a
38	MAX	chr7:8007860-8010956	Hela-S3	cervix:	n/a	chr7:8008789-8008799 chr7:8008803-8008813
39	SIN3AK20	chr7:8007696-8011233	MCF-7	breast:	n/a	n/a
40	YY1	chr7:8010249-8011267	GM12878	blood:	n/a	chr7:8010955-8010971
41	POLR2A	chr7:8006998-8013228	GM12878	blood:	n/a	n/a
42	POLR2A	chr7:8010038-8012279	GM12892	blood:	n/a	n/a
43	RAD21	chr7:8010298-8011064	Hela-S3	cervix:	n/a	chr7:8010822-8010831 chr7:8010835-8010849
44	POLR2A	chr7:8007325-8010927	Raji	blood:	n/a	n/a
45	POLR2A	chr7:8010341-8010531	SK-N-SH	brain:	n/a	n/a
46	BCLAF1	chr7:8010138-8010988	GM12878	blood:	n/a	n/a
47	WRNIP1	chr7:8010182-8012111	GM12878	blood:	n/a	n/a
48	RFX5	chr7:8009342-8011041	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr7:8010338-8011656	GM12891	blood:	n/a	n/a
50	EBF1	chr7:8010115-8010655	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:7947370..7958537-chr7:8006160..8010935,22	MCF-7	breast:
2	chr7:8008267..8011619-chr7:8256762..8258925,4	MCF-7	breast:
3	chr7:7809766..7812689-chr7:8007861..8010451,3	MCF-7	breast:
4	chr7:7679018..7681584-chr7:8008760..8011156,4	K562	blood:
5	chr7:8009265..8011101-chr7:8042338..8044850,2	MCF-7	breast:
6	chr7:8008368..8010705-chr7:8301845..8303366,2	MCF-7	breast:
7	chr7:8010105..8011990-chr7:8023943..8026240,3	MCF-7	breast:
8	chr7:8006834..8014864-chr7:8015250..8023851,23	K562	blood:
9	chr7:8007277..8011687-chr7:8017849..8023164,7	MCF-7	breast:
10	chr7:7988942..7990791-chr7:8008442..8011147,2	K562	blood:

Variant related genes	Relation type
ENSG00000233108	TF binding region
ENSG00000219545	Chromatin interaction
ENSG00000106415	Chromatin interaction
ENSG00000244239	Chromatin interaction
ENSG00000233264	Chromatin interaction
ENSG00000214998	Chromatin interaction
ENSG00000234141	Chromatin interaction
ENSG00000003147	Chromatin interaction
ENSG00000229970	Chromatin interaction
ENSG00000106399	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10226050	0.89[YRI][hapmap]
rs10226865	0.83[MEX][hapmap]
rs10229643	0.90[YRI][hapmap]
rs10243846	0.83[YRI][hapmap]
rs10253861	0.83[MEX][hapmap]
rs10486205	0.90[YRI][hapmap]
rs1476823	0.83[MEX][hapmap]
rs17568389	0.90[YRI][hapmap]
rs2109382	0.82[YRI][hapmap]
rs2191321	0.80[YRI][hapmap]
rs3735457	0.80[YRI][hapmap]
rs37975	0.80[AFR][1000 genomes]
rs37976	0.83[MEX][hapmap]
rs37977	0.81[TSI][hapmap];0.80[YRI][hapmap];0.82[EUR][1000 genomes]
rs37978	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs37981	0.84[MKK][hapmap]
rs37983	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs37988	0.83[YRI][hapmap]
rs37995	0.84[MKK][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes]
rs37998	0.84[LWK][hapmap];0.87[MKK][hapmap];0.80[EUR][1000 genomes]
rs37999	0.80[EUR][1000 genomes]
rs38002	0.83[YRI][hapmap]
rs38003	0.83[MKK][hapmap]
rs38004	0.83[YRI][hapmap]
rs38011	0.83[YRI][hapmap]
rs38012	0.83[ASW][hapmap];0.86[LWK][hapmap];0.86[YRI][hapmap]
rs38013	0.86[LWK][hapmap];0.86[YRI][hapmap]
rs38014	0.90[YRI][hapmap]
rs38018	0.84[LWK][hapmap];0.86[YRI][hapmap]
rs38021	0.83[YRI][hapmap]
rs38022	0.86[YRI][hapmap]
rs4236406	0.83[YRI][hapmap]
rs4725060	0.90[YRI][hapmap]
rs7808399	0.88[MEX][hapmap]
rs9655516	0.88[MEX][hapmap]
rs9692283	0.80[YRI][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	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1020161	chr7:7929384-8047553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs37974	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8007200-8010400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr7:8007200-8010600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:8007200-8010600	Active TSS	Stomach Smooth Muscle	stomach
4	chr7:8007200-8012600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:8007200-8013400	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr7:8007400-8010400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr7:8007400-8010400	Active TSS	Fetal Kidney	kidney
8	chr7:8007400-8010400	Active TSS	NHDF-Ad	bronchial
9	chr7:8007400-8010600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr7:8007400-8010600	Active TSS	NHLF	lung
11	chr7:8007400-8010800	Active TSS	Primary T cells fromperipheralblood	blood
12	chr7:8007400-8010800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:8007400-8011800	Active TSS	Fetal Stomach	stomach
14	chr7:8007400-8012200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr7:8007400-8012200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:8007600-8010400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:8007600-8010400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr7:8007600-8010400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr7:8007600-8010400	Active TSS	HMEC	breast
20	chr7:8007600-8010600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:8007600-8010600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:8007600-8010600	Active TSS	Brain Angular Gyrus	brain
23	chr7:8007600-8010600	Active TSS	Brain Anterior Caudate	brain
24	chr7:8007600-8010600	Active TSS	Fetal Intestine Small	intestine
25	chr7:8007600-8010600	Active TSS	Psoas Muscle	Psoas
26	chr7:8007600-8010600	Active TSS	Right Ventricle	heart
27	chr7:8007600-8011200	Active TSS	Thymus	Thymus
28	chr7:8007600-8011400	Active TSS	GM12878-XiMat	blood
29	chr7:8007600-8011800	Active TSS	Colonic Mucosa	Colon
30	chr7:8007600-8012000	Active TSS	Aorta	Aorta
31	chr7:8007800-8010400	Active TSS	Esophagus	oesophagus
32	chr7:8007800-8010400	Active TSS	Left Ventricle	heart
33	chr7:8007800-8010400	Active TSS	HSMM	muscle
34	chr7:8007800-8010400	Active TSS	HSMMtube	muscle
35	chr7:8007800-8010600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr7:8007800-8010600	Active TSS	H1 Cell Line	embryonic stem cell
37	chr7:8007800-8010600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr7:8007800-8010600	Active TSS	Brain Cingulate Gyrus	brain
39	chr7:8007800-8010600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:8007800-8010600	Active TSS	Placenta Amnion	Placenta Amnion
41	chr7:8007800-8010800	Active TSS	Fetal Muscle Trunk	muscle
42	chr7:8007800-8011200	Active TSS	Placenta	Placenta
43	chr7:8007800-8011400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:8007800-8012000	Active TSS	Ovary	ovary
45	chr7:8008000-8010400	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr7:8008000-8010400	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr7:8008000-8010400	Active TSS	Small Intestine	intestine
48	chr7:8008000-8010400	Active TSS	Hela-S3	cervix
49	chr7:8008000-8010400	Active TSS	NH-A	brain
50	chr7:8008000-8010400	Active TSS	NHEK	skin

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